Direct observation of negative cooperativity in a detoxification enzyme at the atomic level by Electron Paramagnetic Resonance spectroscopy and simulation

The catalytic activity of human glutathione S-transferase A1-1 (hGSTA1-1), a homodimeric detoxification enzyme, is dependent on the conformational dynamics of a key C-terminal helix α9 in each monomer. However, the structural details of how the two monomers interact upon binding of substrates is not well understood and the structure of the ligand-free state of the hGSTA1-1 homodimer has not been resolved. Here, we used a combination of electron paramagnetic resonance (EPR) distance measurements and weighted ensemble (WE) simulations to characterize the conformational ensemble of the ligand-free state at the atomic level. EPR measurements reveal a broad distance distribution between a pair of Cu(II) labels in the ligand-free state that gradually shifts and narrows as a function of increasing ligand concentration. These shifts suggest changes in the relative positioning of the two α9 helices upon ligand binding. WE simulations generated unbiased pathways for the seconds-timescale transition between alternate states of the enzyme, leading to the generation of atomically detailed structures of the ligand-free state. Notably, the simulations provide direct observations of negative cooperativity between the monomers of hGSTA1-1, which involve the mutually exclusive docking of α9 in each monomer as a lid over the active site. We identify key interactions between residues that lead to this negative cooperativity. Negative cooperativity may be essential for interaction of hGSTA1-1 with a wide variety of toxic substrates and their subsequent neutralization. More broadly, this work demonstrates the power of integrating EPR distances with WE rare-events sampling strategy to gain mechanistic information on protein function at the atomic level.

Percentage of intrathoracic stomach predicts operative and post-operative morbidity, persistent reflux and PPI requirement following laparoscopic hiatus hernia repair and fundoplication

PURPOSE

Large hiatus hernias are relatively common and can be associated with adverse symptoms and serious complications. Operative repair is indicated in this patient group for symptom management and the prevention of morbidity. This study aimed to identify predictors of poor outcomes following laparoscopic hiatus hernia repair and fundoplication (LHHRaF) to aid in counselling potential surgical candidates.

METHODOLOGY

A retrospective analysis was performed from a prospectively maintained, multicentre database of patients who underwent LHHRaF between 2014 and 2020. Revision procedures were excluded. Hernia size was defined as the intraoperative percentage of intrathoracic stomach, estimated by the surgeon to the nearest 10%. Predictors of outcomes were determined using a prespecified multivariate logistic regression model.

RESULTS

625 patients underwent LHHRaF between 2014 and 2020 with 443 patients included. Median age was 65 years, 62.9% were female and 42.7% of patients had ≥ 50% intrathoracic stomach. In a multivariate regression model, intrathoracic stomach percentage was predictive of operative complications (P = 0.014, OR 1.05), post-operative complications (P = 0.026, OR 1.01) and higher comprehensive complication index score (P = 0.023, OR 1.04). At 12 months it was predictive of failure to improve symptomatic reflux (P = 0.008, OR 1.02) and persistent PPI requirement (P = 0.047, OR 1.02). Operative duration and blood loss were predicted by BMI (P = 0.004 and < 0.001), Type III/IV hernias (P = 0.045 and P = 0.005) and intrathoracic stomach percentage (P = 0.009 and P < 0.001). Post-operative length of stay was predicted by age (P < 0.001) and emergency presentation (P = 0.003).

CONCLUSION

In a multivariate regression model, intrathoracic stomach percentage was predictive of operative and post-operative morbidity, PPI use, and failure to improve reflux symptoms at 12 months.

#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol

We seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental methods, which are limited in their ability to interrogate aerosols at the atomic/molecular level and thus obscure our understanding of airborne transmission. We demonstrate how our integrated data-driven platform provides a new way of exploring the composition, structure, and dynamics of aerosols and aerosolized viruses, while driving simulation method development along several important axes. We present a series of initial scientific discoveries for the SARS-CoV-2 Delta variant, noting that the full scientific impact of this work has yet to be realized.

Severity of oEsophageal Anastomotic Leak in patients after oesophagectomy: the SEAL score

Background

Anastomotic leak (AL) is a common but severe complication after oesophagectomy. It is unknown how to determine the severity of AL objectively at diagnosis. Determining leak severity may guide treatment decisions and improve future research. This study aimed to identify leak-related prognostic factors for mortality, and to develop a Severity of oEsophageal Anastomotic Leak (SEAL) score.

Methods

This international, retrospective cohort study in 71 centres worldwide included patients with AL after oesophagectomy between 2011 and 2019. The primary endpoint was 90-day mortality. Leak-related prognostic factors were identified after adjusting for confounders and were included in multivariable logistic regression to develop the SEAL score. Four classes of leak severity (mild, moderate, severe, and critical) were defined based on the risk of 90-day mortality, and the score was validated internally.

Results

Some 1509 patients with AL were included and the 90-day mortality rate was 11.7 per cent. Twelve leak-related prognostic factors were included in the SEAL score. The score showed good calibration and discrimination (c-index 0.77, 95 per cent c.i. 0.73 to 0.81). Higher classes of leak severity graded by the SEAL score were associated with a significant increase in duration of ICU stay, healing time, Comprehensive Complication Index score, and Esophagectomy Complications Consensus Group classification.

Conclusion

The SEAL score grades leak severity into four classes by combining 12 leak-related predictors and can be used to the assess severity of AL after oesophagectomy.

#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol

We seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental methods, which are limited in their ability to interrogate aerosols at the atomic/molecular level and thus ob-scure our understanding of airborne transmission. We demonstrate how our integrated data-driven platform provides a new way of exploring the composition, structure, and dynamics of aerosols and aerosolized viruses, while driving simulation method development along several important axes. We present a series of initial scientific discoveries for the SARS-CoV-2 Delta variant, noting that the full scientific impact of this work has yet to be realized.

ACM REFERENCE FORMAT

Abigail Dommer 1† , Lorenzo Casalino 1† , Fiona Kearns 1† , Mia Rosenfeld 1 , Nicholas Wauer 1 , Surl-Hee Ahn 1 , John Russo, 2 Sofia Oliveira 3 , Clare Morris 1 , AnthonyBogetti 4 , AndaTrifan 5,6 , Alexander Brace 5,7 , TerraSztain 1,8 , Austin Clyde 5,7 , Heng Ma 5 , Chakra Chennubhotla 4 , Hyungro Lee 9 , Matteo Turilli 9 , Syma Khalid 10 , Teresa Tamayo-Mendoza 11 , Matthew Welborn 11 , Anders Christensen 11 , Daniel G. A. Smith 11 , Zhuoran Qiao 12 , Sai Krishna Sirumalla 11 , Michael O'Connor 11 , Frederick Manby 11 , Anima Anandkumar 12,13 , David Hardy 6 , James Phillips 6 , Abraham Stern 13 , Josh Romero 13 , David Clark 13 , Mitchell Dorrell 14 , Tom Maiden 14 , Lei Huang 15 , John McCalpin 15 , Christo- pherWoods 3 , Alan Gray 13 , MattWilliams 3 , Bryan Barker 16 , HarindaRajapaksha 16 , Richard Pitts 16 , Tom Gibbs 13 , John Stone 6 , Daniel Zuckerman 2 *, Adrian Mulholland 3 *, Thomas MillerIII 11,12 *, ShantenuJha 9 *, Arvind Ramanathan 5 *, Lillian Chong 4 *, Rommie Amaro 1 *. 2021. #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy ofDeltaSARS-CoV-2 in a Respiratory Aerosol. In Supercomputing '21: International Conference for High Perfor-mance Computing, Networking, Storage, and Analysis . ACM, New York, NY, USA, 14 pages. https://doi.org/finalDOI.

AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics

We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. We use this workflow to investigate the mechanisms of infectivity of the SARS-CoV-2 spike protein, the main viral infection machinery. Our workflow enables more efficient investigation of spike dynamics in a variety of complex environments, including within a complete SARS-CoV-2 viral envelope simulation, which contains 305 million atoms and shows strong scaling on ORNL Summit using NAMD. We present several novel scientific discoveries, including the elucidation of the spike's full glycan shield, the role of spike glycans in modulating the infectivity of the virus, and the characterization of the flexible interactions between the spike and the human ACE2 receptor. We also demonstrate how AI can accelerate conformational sampling across different systems and pave the way for the future application of such methods to additional studies in SARS-CoV-2 and other molecular systems.

Population fluctuations of light-attracted chrysomelid beetles in relation to supra-annual environmental changes in a Bornean rainforest

In Southeast Asian tropical rainforests, two events, severe droughts associated with the El Niño-Southern Oscillation and general flowering, a type of community-wide mass flowering, occur at irregular, supra-annual intervals. The relationship between these two supra-annual events and patterns of insect population fluctuations has yet to be clearly elucidated. Leaf beetles (Chrysomelidae) are major herbivores and flower-visitors of canopy trees, affecting their growth and reproduction and, in turn, affected by tree phenology; but their population fluctuations in the Southeast Asian tropics have not been extensively investigated. We examined population fluctuation patterns of the 34 most dominant chrysomelid species in relation to the two supra-annual events by conducting monthly light-trapping over seven years in a lowland dipterocarp forest in Borneo. Our results showed large community variation in population fluctuation patterns and a supra-annual (between-year) variation in abundance for most of the dominant chrysomelids that was significantly larger than the annual (within-year) variation. Specifically, in response to a severe drought in 1998, chrysomelid species exhibited different population responses. These results show that population fluctuations of individual species, rather than the entire assemblage, must be analyzed to determine the effects of changes in environmental conditions on the structure of insect assemblages in the tropics, especially in regions where supra-annual environmental changes are relatively more important than seasonal changes.

Basal cell carcinoma of the nose: an Australian and New Zealand radiation oncology patterns-of-practice study

Patients with a basal cell carcinoma (BCC) of the nose may be recommended radiotherapy (RT) with a wide variation in techniques and prescribed dose fractionation schedules between clinicians. The aim of this study was to ascertain variability in the patterns of practice among Australian and New Zealand radiation oncologists (ROs) when treating BCC arising on the nose. A postal survey was sent to 222 practising ANZ ROs detailing 12 different clinical scenarios of a BCC arising on the nose. The treatment selected for each scenario was analysed according to clinician's attitudes, training, experience and the availability of resources. The response rate was 74% (165/222) with 90 respondents treating non-melanoma skin cancer. Training was perceived to have a marked influence on treatment practice by most (79%). In total, 72% of ROs were 'very certain' in their choice of a dose fractionation schedule for obtaining local control and 61% for a satisfactory cosmetic outcome, respectively. Most (76%) favoured low-voltage photons over electrons as the optimal method of treatment, although for certain clinical scenarios most would use electrons. Dose fractionation schedules were highly variable with a lower total dose and hypofractionation favoured for older patients. Low-voltage photons were favoured for the T1 BCC and electrons for the T2 and T4 BCC. Nearly one-third of the ROs chose megavoltage photons for the T4 lesion. There is marked variation in treatment practices in terms of recommending RT over other treatment options, the choice of RT method, the dose fractionation schedule, the extent of field margins and the point of dose prescription.

47 SUCCESSFULLY PRODUCING CLONED MICE FROM SOMATIC CELLS OF AGED MICE VIA ESTABLISHED ntES CELL LINES

Recent nuclear transfer techniques have enabled us to produce cloned animals from somatic cell nuclei in a variety of animal species and are to date the only way to obtain offspring from infertile animals. Despite very aged mice often showing an infertile phenotype, the decreasing rate of cloning success with increased age makes it almost impossible to produce cloned mice or offspring from these animals. Other studies, however, have demonstrated that ES cell lines have been established from cloned blastocysts through somatic cell nuclear transfer (ntES cells), irrespective of sex, strains, or organs. These cells are subsequently capable of differentiating into all three germ layers in vitro, or even into spermatozoa and oocytes in chimeric mice. Thus, ntES cells have received considerable attention recently in regenerative medicine. Importantly, the success rate of establishing ntES cell lines from cloned blastocysts is ten times higher than that of producing cloned mice, which may allow us to establish ntES cell lines even from such 'unclonable' aged mice. ntES cells also have the potential to be a good donor source for nuclear transfer as they have the same DNA as their donor somatic cells and can indefinitely proliferate in their undifferentiated states. In this study, we attempted to establish ntES cell lines from aged mice and analyze their normality. We then tried to produce cloned mice via nuclear transfer using established ntES cell lines. We obtained donor cells from tail-tip fibroblast cells of BDF1 and BCF1 male and female mice that were over two years old. Following nuclear transfer, we transferred a proportion of the cleaved cloned embryos to pseudopregnant ICR female mice. The remaining embryos were cultured for 72 h, and cloned embryos that developed into morulae or blastocysts were plated on feeder cells. We then examined all established ntES cell lines for normality by Oct4 and Nanog expression using immunofluorescence staining and pluripotency by chimeric mice formation, for which ntES cells were injected into fertilized ICR embryos. Finally, we attempted to produce cloned mice from the nuclei of these ntES cell lines. In each experiment, 25, 37, 73, 63, and 75 cloned embryos from aged mice tail-tip cells were used in attempts to produce cloned mice, and 20, 20, 27, 35, and 40 cloned embryos were used to derive ntES cell lines, respectively. No cloned mice were obtained by direct nuclear transfer of the aged mice tail-tip cells; however, we were successful in establishing ntES cell lines from all experiments, with an establishment rate between 10 and 25%. All established ntES cell lines expressed Oct4 and Nanog and contributed to somatic cells in chimeric mice. Some chimeric mice produced offspring derived from ntES cells after mating. We were also able to produce cloned mice even from a 2-year-old and a 9-month-old BCF1 male mouse by nuclear transfer using ntES cells as donor nuclei. These results clearly show that normal ntES cell lines can be established from infertile, aged mice and this technique can now be used to produce offspring, irrespective of donor conditions.

Matrix metalloproteinases and aggrecanases cleave aggrecan in different zones of normal cartilage but colocalize in the development of osteoarthritic lesions in STR/ort mice

OBJECTIVE

To map aggrecan cleavage by matrix metalloproteinases (MMPs) and aggrecanases in normal murine tibial articular cartilage (CBA strain) and in the development of spontaneous osteoarthritis (OA) in the STR/ort mouse and to assess the influence of sex hormone status on these conditions in gonadectomized STR/ort mice.

METHODS

The distributions of neoepitopes of aggrecan generated by MMP (VDIPEN) and aggrecanase (NITEGE) cleavage were investigated by immunohistochemistry.

RESULTS

VDIPEN neoepitope was detected mainly in the pericellular matrix of deep-zone chondrocytes in normal tibial cartilage from STR/ort and CBA mice. In early OA, VDIPEN immunostaining also localized to the pericellular matrix of chondrocytes at the site of the lesion. With increasing severity of OA lesions, VDIPEN immunostaining was also detected in the interterritorial matrix, close to the site of the lesion. In contrast, NITEGE mapped most strongly to the pericellular matrix of upper-zone chondrocytes in normal tibial cartilage. As with VDIPEN, NITEGE was strongly expressed in the pericellular matrix at the site of early OA lesions. With advancing OA, NITEGE colocalized with VDIPEN in both the pericellular and interterritorial matrices of chondrocytes adjacent to OA lesions and in those of the deep zones. Hormone status did not appear to influence the development of OA or the distribution of aggrecan neoepitopes in STR/ort mice.

CONCLUSION

MMP- and aggrecanase-generated neoepitopes map predominantly to different regions in normal murine tibial cartilage. However, both groups of enzymes generate increased amounts of neoepitopes in pericellular and interterritorial matrix adjacent to histopathologic lesions of OA. Aggrecan degradation and the development of OA appear to be independent of sex hormone status in this model.

Treatment planning and delivery of intensity-modulated radiation therapy for primary nasopharynx cancer

PURPOSE

To implement intensity-modulated radiation therapy (IMRT) for primary nasopharynx cancer and to compare this technique with conventional treatment methods.

METHODS AND MATERIALS

Between May 1998 and June 2000, 23 patients with primary nasopharynx cancer were treated with IMRT delivered with dynamic multileaf collimation. Treatments were designed using an inverse planning algorithm, which accepts dose and dose-volume constraints for targets and normal structures. The IMRT plan was compared with a traditional plan consisting of phased lateral fields and a three-dimensional (3D) plan consisting of a combination of lateral fields and a 3D conformal plan.

RESULTS

Mean planning target volume (PTV) dose increased from 67.9 Gy with the traditional plan, to 74.6 Gy and 77.3 Gy with the 3D and IMRT plans, respectively. PTV coverage improved in the parapharyngeal region, the skull base, and the medial aspects of the nodal volumes using IMRT and doses to all normal structures decreased compared to the other treatment approaches. Average maximum cord dose decreased from 49 Gy with the traditional plan, to 44 Gy with the 3D plan and 34.5 Gy with IMRT. With the IMRT plan, the volume of mandible and temporal lobes receiving more than 60 Gy decreased by 10-15% compared to the traditional and 3D plans. The mean parotid gland dose decreased with IMRT, although it was not low enough to preserve salivary function.

CONCLUSION

Lower normal tissue doses and improved target coverage, primarily in the retropharynx, skull base, and nodal regions, were achieved using IMRT. IMRT could potentially improve locoregional control and toxicity at current dose levels or facilitate dose escalation to further enhance locoregional control.

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

A historical perspective on the application of molecular dynamics (MD) to biological macromolecules is presented. Recent developments combining state-of-the-art force fields with continuum solvation calculations have allowed us to reach the fourth era of MD applications in which one can often derive both accurate structure and accurate relative free energies from molecular dynamics trajectories. We illustrate such applications on nucleic acid duplexes, RNA hairpins, protein folding trajectories, and protein-ligand, protein-protein, and protein-nucleic acid interactions.

Vasoactive and proliferative effects of parathyroid hormone and parathyroid hormone-related peptide on human vascular smooth muscle

BACKGROUND

Hyperparathyroidism is associated with an increased incidence of hypertension and cardiovascular disease. Experiments in rats suggest that this results from desensitization of the normally inhibitory effects of parathyroid hormone-related peptide (PTHrP) on vascular smooth muscle cells (VSMCs) by previous exposure to parathyroid hormone (PTH).

METHODS

Isometric tension in vitro was measured in segments of vessels obtained at neck surgery from six normotensive patients with hyperparathyroidism and 12 eucalcaemic controls undergoing thyroid surgery. Vessels were precontracted with noradrenaline to allow the vasodilatory effects of PTH and PTHrP to be observed. Human VSMCs were cultured in 0.5, 5 and 15 per cent serum with or without PTH (10(-11) to 10(-7) nmol l-(1)) and proliferation was assessed by cell counts after 14 days.

RESULTS

Vasodilatation of arterial segments produced by both PTH 20 nmol l(-1) and PTHrP 100 nmol l(-1) did not differ significantly between control and hyperparathyroidism groups (P > 0.08, Mann-Whitney U test). Vasodilatation by PTHrP was not reduced by preincubation of vessels in vitro with PTH 50 nmol l(-1) for 1 h (P > 0.36, Wilcoxon test). No effects of PTH on serum-induced proliferation of human VSMCs were observed.

CONCLUSION

These data imply that homologous desensitization to PTHrP is not implicated in the pathogenesis of vascular disease in patients with hyperparathyroidism.

Human telomeres contain two distinct Myb-related proteins, TRF1 and TRF2

Human telomeres are composed of long arrays of TTAGGG repeats that form a nucleoprotein complex required for the protection and replication of chromosome ends. One component of human telomeres is the TTAGGG repeat binding factor 1 (TRF1), a ubiquitously expressed protein, related to the protooncogene Myb, that is present at telomeres throughout the cell cycle. Recent evidence has implicated TRF1 in the control of telomere length. TRF1 is proposed to be an inhibitor of telomerase, acting in cis to limit the elongation of individual chromosome ends. Here we report the cloning of TRF2, a distant homologue of TRF1 that carries a very similar Myb-related DNA-binding motif. Like TRF1, TRF2 was ubiquitously expressed, bound specifically to duplex TTAGGG repeats in vitro and localized to all human telomeres in metaphase chromosomes. TRF2 was shown to have an architecture similar to that of TRF1 in that it carries a C-terminal Myb motif and a large TRF1-related dimerization domain near its N terminus. However, the dimerization domains of TRF1 and TRF2 did not interact, suggesting that these proteins exist predominantly as homodimers. While having similar telomere binding activity and domain organization, TRF2 differed from TRF1 in that its N terminus was basic rather than acidic, and TRF2 was much more conserved than TRF1. The results indicate that the TTAGGG repeat arrays at the ends of human and mouse chromosomes bind to two related proteins. Because TRF1 and TRF2 showed significant differences, we suggest that these factors have distinct functions at telomeres.

Identification of XLerk, an Eph family ligand regulated during mesoderm induction and neurogenesis in Xenopus laevis

We have isolated and characterized the first Xenopus transmembrane Eph ligand, XLerk (Xenopus Ligand for Eph Receptor Tyrosine Kinases). While this ligand has 72% identity with the closest mammalian family member, Lerk-2, it is the cytoplasmic domain of this molecule that is the most conserved domain with 95% identity. XLerk exists as a maternally expressed mRNA, however, expression of transcripts and protein increase during gastrulation and again in the late swimming tadpole stage. In the adult, XLerk is expressed at low levels in most adult tissues with increased levels observed in the kidney, oocytes, ovary and testis. While low levels of XLerk expression are observed in the adult brain, in situ hybridization analysis demonstrates prominent expression in the developing olfactory system, retina, hindbrain, cranial ganglia, and somites. Furthermore, we have shown that XLerk transcripts are significantly elevated during mesoderm induction caused by activin and FGF, but not during noggin-induced neuralization. These results suggest a role for XLerk in the developing mesenchymal and nervous tissue.

Oral lymphoma in HIV infection

OBJECTIVE

This study reports the main clinical and histological features, and the treatment and outcomes of six HIV-associated oral lymphomas.

SUBJECTS

During the period 1991-1995, six cases of lymphoma presenting in the oral cavity were diagnosed in this clinic. All six patients were men ranging in age from 36 to 62 years with CD4 counts below 100 cells mm-3.

RESULTS

In five patients, oral lymphoma was the first AIDS defining disease. Four lesions occurred on the gingiva, one on the palate and one on the tongue. The duration of symptoms prior to presentation ranged from 2 weeks to 14 months. In all but one patient, the lesions presented as red, exophytic masses and were diagnosed clinically as Kaposi's sarcoma. None of the five lesions presenting on the palate or gingiva showed radiographic evidence of bone destruction. Metastatic work-up failed to diagnose lymphoma elsewhere in the five cases where this was performed. Histological diagnoses included two small, non-cleaved (Burkitt's type) lymphomas, two immunoblastic lymphomas, one large cell lymphoma and one small, non-cleaved (non-Burkitt's) lymphoma.

CONCLUSION

These findings highlight the uncommon clinical presentation of this disease and despite its relative rarity, demonstrate the need to maintain a high degree of suspicion in any unusual oral lesion in this group of patients.

TRF1 is a dimer and bends telomeric DNA

TRF1 is a mammalian telomeric protein that binds to the duplex array of TTAGGG repeats at chromosome ends. TRF1 has homology to the DNA-binding domain of the Myb family of transcription factors but, unlike most Myb-related proteins, TRF1 carries one rather than multiple Myb-type DNA-binding motifs. Here we show that TRF1 binds DNA as a dimer using a large conserved domain near the N-terminus of the protein for TRF1-TRF1 interactions. Dimerization was observed both in a complex with DNA and in the yeast two-hybrid assay. TRF1 dimers were found to require both Myb repeats for the formation of a stable complex with DNA, indicating a parallel between the DNA-binding mode of TRF1 and other Myb-related proteins. TRF1 was found to have a number of biochemical similarities to Rap1p, a distantly related DNA-binding protein that functions at telomeres in yeast. Rap1p and TRF1 both require two Myb motifs for DNA binding and both factors bind along their cognate telomeric sequences without showing strong cooperative interactions between adjacent proteins. Furthermore, TRF1 was found to bend its telomeric site to an angle of -120 degrees. Since Rap1p similarly distorts telomeric DNA, we propose that DNA bending is important for the function of telomeres in yeast and mammals.

Comparison of the human and mouse genes encoding the telomeric protein, TRF1: chromosomal localization, expression and conserved protein domains

Mammalian chromosome ends contain long arrays of TTAGGG repeats that are complexed to a telomere specific protein, the TTAGGG repeat binding factor, TRF1. Here we describe the characterization of genes encoding the human and mouse TRF1 proteins, hTRF1 and mTRF1. The mTRF1 cDNA was isolated based on sequence similarity to the hTRF1 cDNA and the mTRF1 mRNA was shown to be ubiquitously expressed as a single 1.9 kb polyadenylated transcript in mouse somatic tissues. High levels of a 2.1 kb transcript were found in testes. In vitro translation of the mTRF1 cDNA resulted in a 56 kDa protein that binds to TTAGGG repeat arrays. mTRF1 displayed the same sequence specificity as hTRF1, preferring arrays of TTAGGG repeats as a binding substrate over TTAGGC and TTGGGG repeats. Expression of an epitope-tagged version of mTRF1 showed that the protein is located at the ends of murine metaphase chromosomes. In agreement, conceptual translation indicated that mTRF1 and hTRF1 are similarly-sized proteins with nearly identical C-terminal Myb-related DNA binding motifs. In addition, comparison of the predicted mTRF1 and hTRF1 amino acid sequences showed that the acidic nature of the N-terminus of TRF1 is conserved and revealed a highly conserved novel domain of approximately 200 amino acids in the middle of the proteins. However, other regions of the proteins are poorly conserved (<35% identity) and the overall level of identity of the mTRF1 and hTRF1 amino acid sequences is only 67%. The TRF1 genes are not syntenic; the hTRF1 gene localized to human chromosome 8 band q13 while the mTRF1 gene localized to mouse chromosome 17 band E3. The data indicate that the genes for mammalian telomeric proteins evolve rapidly.

Structure, subnuclear distribution, and nuclear matrix association of the mammalian telomeric complex

Mammalian telomeres are composed of long arrays of TTAGGG repeats complexed with the TTAGGG repeat binding factor, TRF. Biochemical and ultrastructural data presented here show that the telomeric DNA and TRF colocalize in individual, condensed structures in the nuclear matrix. Telomeric TTAGGG repeats were found to carry an array of nuclear matrix attachment sites occurring at a frequency of at least one per kb. The nuclear matrix association of the telomeric arrays extended over large domains of up to 20-30 kb, encompassing the entire length of most mammalian telomeres. TRF protein and telomeric DNA cofractionated in nuclear matrix preparations and colocalized in discrete, condensed sites throughout the nuclear volume. FISH analysis indicated that TRF is an integral component of the telomeric complex and that the presence of TRF on telomeric DNA correlates with the compact configuration of telomeres and their association with the nuclear matrix. Biochemical fractionation of TRF and telomeric DNA did not reveal an interaction with the nuclear lamina. Furthermore, ultrastructural analysis indicated that the mammalian telomeric complex occupied sites throughout the nuclear volume, arguing against a role for the nuclear envelope in telomere function during interphase. These results are consistent with the view that mammalian telomeres form nuclear matrix-associated, TRF-containing higher order complexes at dispersed sites throughout the nuclear volume.

A human telomeric protein

Telomeres are multifunctional elements that shield chromosome ends from degradation and end-to-end fusions, prevent activation of DNA damage checkpoints, and modulate the maintenance of telomeric DNA by telomerase. A major protein component of human telomeres has been identified and cloned. This factor, TRF, contains one Myb-type DNA-binding repeat and an amino-terminal acidic domain. Immunofluorescent labeling shows that TRF specifically colocalizes with telomeric DNA in human interphase cells and is located at chromosome ends during metaphase. The presence of TRF along the telomeric TTAGGG repeat array demonstrates that human telomeres form a specialized nucleoprotein complex.

Glycoprotein cytoplasmic domain sequences required for rescue of a vesicular stomatitis virus glycoprotein mutant

We have used transient expression of the wild-type vesicular stomatitis virus (VSV) glycoprotein (G protein) from cloned cDNA to rescue a temperature-sensitive G protein mutant of VSV in cells at the nonpermissive temperature. Using cDNAs encoding G proteins with deletions in the normal 29-amino-acid cytoplasmic domain, we determined that the presence of either the membrane-proximal 9 amino acids or the membrane-distal 12 amino acids was sufficient for rescue of the temperature-sensitive mutant. G proteins with cytoplasmic domains derived from other cellular or viral G proteins did not rescue the mutant, nor did G proteins with one or three amino acids of the normal cytoplasmic domain. Rescue correlated directly with the ability of the G proteins to be incorporated into virus particles. This was shown by analysis of radiolabeled particles separated on sucrose gradients as well as by electron microscopy of rescued virus after immunogold labeling. Quantitation of surface expression showed that all of the mutated G proteins were expressed less efficiently on the cell surface than was wild-type G protein. However, we were able to correct for differences in rescue efficiency resulting from differences in the level of surface expression by reducing wild-type G protein expression to levels equivalent to those observed for the mutated G proteins. Our results provide evidence that at least a portion of the cytoplasmic domain is required for efficient assembly of the VSV G protein into virions during virus budding.

Gnathotrichus sulcatus: synergistic response to enantiomers of the aggregation pheromone sulcatol

In laboratory and field bioassays, Gnathotrichus sulcatus responded to sulcatol (6-methyl-5-hepten-2-ol) only when both enantiomers were present. Response was greater to racemic sulcatol than to a mixture (65 : 35) of S-(+) and R-(-) enantiomers, the naturally occurring isomeric ratio. Enantiomer-specific active sites on receptor proteins in the same or different cells are implicated.