Protein structure and conformational changes studied by Fourier transform infrared spectroscopy

Fourier transform infrared spectroscopy (FTIR) has been used to study a range of different proteins. These include:- i) Human serum transferrin, human lactoferrin and rabbit serum transferrin. A study has been made of the structural changes that accompany iron binding and release from these related proteins. Structural variations within this group of proteins have been shown. Thermal denaturation studies, using differential scanning calorimetric measurements, have been related to FTIR spectral changes and indicate that the crystal structure of iron-free human lactoferrin may not reflect the structure of this protein in solution. ii) Human placental transferrin receptor. This protein has been examined at extracellular and endosomal pH. Both the intact protein in detergent and its water soluble major extracellular fragment have been investigated. iii) The bacterial adhesive protein streptococcal antigen I/II. The solution structure and thermal stability of the native protein, the recombinant full-length protein and four recombinant fragments of this protein have been examined using both Fourier transform infrared spectroscopy and circular dichroism spectroscopy. iv) Albumin, IgG, Ribonuclease, Fibrinogen, A study of the thermal stability of these and other proteins has been undertaken to compare their denaturation properties in H2O and 2H2O solutions. v) Lysozyme, Ribonuclease These and several other proteins have been examined using Fourier transform infrared microscopy in order to compare the infrared spectra of these proteins, both in solution and also in the form of single crystals. Many of the proteins show similar spectra, whether recorded in solution or from a single crystal. In some cases, as with single crystals oi Endothia parasitica pepsin, Mucor pucillus pepsin and serum amyloid P component, the spectra differ from those recorded in solution. These differences may indicate that a rearrangement of turns structures occurs upon crystallisation. The major novel findings of this work are: i) There are small but significant structural differences between human serum transferrin, rabbit serum transferrin and human lactoferrin. The crystal structure of human lactoferrin may not represent the structure of this protein in solution. The apparent conflict between CD, FTIR and X-ray crystallographic estimates of secondary structural content of the transferrins can be explained by the fact that CD estimates are based on dihedral angles and not hydrogen bonding patterns. ii) Intact transferrin receptor precipitates out of solution at endosomal pH while the extracellular fragment remains soluble but undergoes a conformational change. This results in minor change in the secondary structural content of the protein and a reduction of thermal stability by approximately 15°C. iii) The recombinant polypeptides produced to study the structure of streptococcal antigen I/II have been shown to fold into defined secondary structures. Furthermore the structures of these fragments have been used to predict a possible structure for the native protein. iv) Quantitative analysis of thermally induced changes in the FTIR spectra of proteins in H2O solution may not offer any significant advantage to analyses performed in 2H2O due to problems associated with the different molar absorption coefficients of the separate secondary structures in H2O solution. v) Infrared spectroscopy/microscopy can be successfully be applied to the study of protein structure in both the solution and crystalline form

Scheduling with partial orders and a causal model

In an ongoing project at Honeywell SRC, we are constructing a prototype scheduling system for a NASA domain using the 'Time Map Manager' (TMM). The TMM representations are flexible enough to permit the representation of precedence constraints, metric constraints between activities, and constraints relative to a variety of references (e.g., Mission Elapsed Time vs. Mission Day). The TMM also supports a simple form of causal reasoning (projection), dynamic database updates, and monitoring specified database properties as changes occur over time. The greatest apparent advantage to using the TMM is the flexibility added to the scheduling process: schedules are constructed by a process of 'iterative refinement,' in which scheduling decisions correspond to constraining an activity either with respect to another activity or with respect to one time line. The schedule becomes more detailed as activities and constraints are added. Undoing a scheduling decision means removing a constraint, not removing an activity from a specified place on the time line. For example, we can move an activity around on the time line by deleting constraints and adding new ones

REV1 Inhibition Enhances Radioresistance and Autophagy

SIMPLE SUMMARY: Cancer resistance to therapy continues to be the biggest challenge in treating patients. Targeting the mutagenic translesion synthesis (TLS) polymerase REV1 was previously shown to sensitize cancer cells to chemotherapy. In this study, we tested the ability of REV1 inhibitors to radiation therapy and observed a lack of radiosensitization. In addition, we observed REV1 inhibition to trigger an autophagy stress response. Because reduction of REV1 triggered autophagy and failed to radiosensitize cells, we hypothesize REV1 expression dynamics might link cancer cell response to radiation treatment through the potential induction of autophagy. ABSTRACT: Cancer therapy resistance is a persistent clinical challenge. Recently, inhibition of the mutagenic translesion synthesis (TLS) protein REV1 was shown to enhance tumor cell response to chemotherapy by triggering senescence hallmarks. These observations suggest REV1’s important role in determining cancer cell response to chemotherapy. Whether REV1 inhibition would similarly sensitize cancer cells to radiation treatment is unknown. This study reports a lack of radiosensitization in response to REV1 inhibition by small molecule inhibitors in ionizing radiation-exposed cancer cells. Instead, REV1 inhibition unexpectedly triggers autophagy, which is a known biomarker of radioresistance. We report a possible role of the REV1 TLS protein in determining cancer treatment outcomes depending upon the type of DNA damage inflicted. Furthermore, we discover that REV1 inhibition directly triggers autophagy, an uncharacterized REV1 phenotype, with a significant bearing on cancer treatment regimens

Social stratification without genetic differentiation at the site of Kulubnarti in Christian Period Nubia

Relatively little is known about Nubia’s genetic landscape prior to the influence of the Islamic migrations that began in the late 1st millennium CE. Here, we increase the number of ancient individuals with genome-level data from the Nile Valley from three to 69, reporting data for 66 individuals from two cemeteries at the Christian Period (~650–1000 CE) site of Kulubnarti, where multiple lines of evidence suggest social stratification. The Kulubnarti Nubians had ~43% Nilotic-related ancestry (individual variation between ~36–54%) with the remaining ancestry consistent with being introduced through Egypt and ultimately deriving from an ancestry pool like that found in the Bronze and Iron Age Levant. The Kulubnarti gene pool – shaped over a millennium – harbors disproportionately female-associated West Eurasian-related ancestry. Genetic similarity among individuals from the two cemeteries supports a hypothesis of social division without genetic distinction. Seven pairs of inter-cemetery relatives suggest fluidity between cemetery groups. Present-day Nubians are not directly descended from the Kulubnarti Nubians, attesting to additional genetic input since the Christian Period.K.A.S. was supported by a Doctoral Dissertation Research Improvement Grant from the National Science Foundation (BCS-1613577). D.R. was funded by NSF HOMINID grant BCS-1032255; NIH (NIGMS) grant GM100233; the Allen Discovery Center program, a Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation; the John Templeton Foundation grant 61220; and the Howard Hughes Medical Institute

A Compact Multi-Planet System With A Significantly Misaligned Ultra Short Period Planet

We report the discovery of a compact multi-planet system orbiting the relatively nearby (78pc) and bright ($K=8.9$) K-star, K2-266 (EPIC248435473). We identify up to six possible planets orbiting K2-266 with estimated periods of P$_b$ = 0.66, P$_{.02}$ = 6.1, P$_c$ = 7.8, P$_d$ = 14.7, P$_e$ = 19.5, and P$_{.06}$ = 56.7 days and radii of R$_P$ = 3.3 R$_{\oplus}$, 0.646 R$_{\oplus}$, 0.705 R$_{\oplus}$, 2.93 R$_{\oplus}$, 2.73 R$_{\oplus}$, and 0.90 R$_{\oplus}$, respectively. We are able to confirm the planetary nature of two of these planets (d & e) from analyzing their transit timing variations ($m_d= 8.9_{-3.8}^{+5.7} M_\oplus$ and $m_e=14.3_{-5.0}^{+6.4} M_\oplus$), confidently validate the planetary nature of two other planets (b & c), and classify the last two as planetary candidates (K2-266.02 & .06). From a simultaneous fit of all 6 possible planets, we find that K2-266 b's orbit has an inclination of 75.32$^{\circ}$ while the other five planets have inclinations of 87-90$^{\circ}$. This observed mutual misalignment may indicate that K2-266 b formed differently from the other planets in the system. The brightness of the host star and the relatively large size of the sub-Neptune sized planets d and e make them well-suited for atmospheric characterization efforts with facilities like the Hubble Space Telescope and upcoming James Webb Space Telescope. We also identify an 8.5-day transiting planet candidate orbiting EPIC248435395, a co-moving companion to K2-266.Comment: 18 pages, 12 figures, 7 tables, Accepted for Publication in the Astronomical Journa

Cognitive behavioural therapy for adults with dissociative seizures (CODES): a pragmatic, multicentre, randomised controlled trial.

BACKGROUND: Dissociative seizures are paroxysmal events resembling epilepsy or syncope with characteristic features that allow them to be distinguished from other medical conditions. We aimed to compare the effectiveness of cognitive behavioural therapy (CBT) plus standardised medical care with standardised medical care alone for the reduction of dissociative seizure frequency. METHODS: In this pragmatic, parallel-arm, multicentre randomised controlled trial, we initially recruited participants at 27 neurology or epilepsy services in England, Scotland, and Wales. Adults (≥18 years) who had dissociative seizures in the previous 8 weeks and no epileptic seizures in the previous 12 months were subsequently randomly assigned (1:1) from 17 liaison or neuropsychiatry services following psychiatric assessment, to receive standardised medical care or CBT plus standardised medical care, using a web-based system. Randomisation was stratified by neuropsychiatry or liaison psychiatry recruitment site. The trial manager, chief investigator, all treating clinicians, and patients were aware of treatment allocation, but outcome data collectors and trial statisticians were unaware of treatment allocation. Patients were followed up 6 months and 12 months after randomisation. The primary outcome was monthly dissociative seizure frequency (ie, frequency in the previous 4 weeks) assessed at 12 months. Secondary outcomes assessed at 12 months were: seizure severity (intensity) and bothersomeness; longest period of seizure freedom in the previous 6 months; complete seizure freedom in the previous 3 months; a greater than 50% reduction in seizure frequency relative to baseline; changes in dissociative seizures (rated by others); health-related quality of life; psychosocial functioning; psychiatric symptoms, psychological distress, and somatic symptom burden; and clinical impression of improvement and satisfaction. p values and statistical significance for outcomes were reported without correction for multiple comparisons as per our protocol. Primary and secondary outcomes were assessed in the intention-to-treat population with multiple imputation for missing observations. This trial is registered with the International Standard Randomised Controlled Trial registry, ISRCTN05681227, and ClinicalTrials.gov, NCT02325544. FINDINGS: Between Jan 16, 2015, and May 31, 2017, we randomly assigned 368 patients to receive CBT plus standardised medical care (n=186) or standardised medical care alone (n=182); of whom 313 had primary outcome data at 12 months (156 [84%] of 186 patients in the CBT plus standardised medical care group and 157 [86%] of 182 patients in the standardised medical care group). At 12 months, no significant difference in monthly dissociative seizure frequency was identified between the groups (median 4 seizures [IQR 0-20] in the CBT plus standardised medical care group vs 7 seizures [1-35] in the standardised medical care group; estimated incidence rate ratio [IRR] 0·78 [95% CI 0·56-1·09]; p=0·144). Dissociative seizures were rated as less bothersome in the CBT plus standardised medical care group than the standardised medical care group (estimated mean difference -0·53 [95% CI -0·97 to -0·08]; p=0·020). The CBT plus standardised medical care group had a longer period of dissociative seizure freedom in the previous 6 months (estimated IRR 1·64 [95% CI 1·22 to 2·20]; p=0·001), reported better health-related quality of life on the EuroQoL-5 Dimensions-5 Level Health Today visual analogue scale (estimated mean difference 6·16 [95% CI 1·48 to 10·84]; p=0·010), less impairment in psychosocial functioning on the Work and Social Adjustment Scale (estimated mean difference -4·12 [95% CI -6·35 to -1·89]; p<0·001), less overall psychological distress than the standardised medical care group on the Clinical Outcomes in Routine Evaluation-10 scale (estimated mean difference -1·65 [95% CI -2·96 to -0·35]; p=0·013), and fewer somatic symptoms on the modified Patient Health Questionnaire-15 scale (estimated mean difference -1·67 [95% CI -2·90 to -0·44]; p=0·008). Clinical improvement at 12 months was greater in the CBT plus standardised medical care group than the standardised medical care alone group as reported by patients (estimated mean difference 0·66 [95% CI 0·26 to 1·04]; p=0·001) and by clinicians (estimated mean difference 0·47 [95% CI 0·21 to 0·73]; p<0·001), and the CBT plus standardised medical care group had greater satisfaction with treatment than did the standardised medical care group (estimated mean difference 0·90 [95% CI 0·48 to 1·31]; p<0·001). No significant differences in patient-reported seizure severity (estimated mean difference -0·11 [95% CI -0·50 to 0·29]; p=0·593) or seizure freedom in the last 3 months of the study (estimated odds ratio [OR] 1·77 [95% CI 0·93 to 3·37]; p=0·083) were identified between the groups. Furthermore, no significant differences were identified in the proportion of patients who had a more than 50% reduction in dissociative seizure frequency compared with baseline (OR 1·27 [95% CI 0·80 to 2·02]; p=0·313). Additionally, the 12-item Short Form survey-version 2 scores (estimated mean difference for the Physical Component Summary score 1·78 [95% CI -0·37 to 3·92]; p=0·105; estimated mean difference for the Mental Component Summary score 2·22 [95% CI -0·30 to 4·75]; p=0·084), the Generalised Anxiety Disorder-7 scale score (estimated mean difference -1·09 [95% CI -2·27 to 0·09]; p=0·069), and the Patient Health Questionnaire-9 scale depression score (estimated mean difference -1·10 [95% CI -2·41 to 0·21]; p=0·099) did not differ significantly between groups. Changes in dissociative seizures (rated by others) could not be assessed due to insufficient data. During the 12-month period, the number of adverse events was similar between the groups: 57 (31%) of 186 participants in the CBT plus standardised medical care group reported 97 adverse events and 53 (29%) of 182 participants in the standardised medical care group reported 79 adverse events. INTERPRETATION: CBT plus standardised medical care had no statistically significant advantage compared with standardised medical care alone for the reduction of monthly seizures. However, improvements were observed in a number of clinically relevant secondary outcomes following CBT plus standardised medical care when compared with standardised medical care alone. Thus, adults with dissociative seizures might benefit from the addition of dissociative seizure-specific CBT to specialist care from neurologists and psychiatrists. Future work is needed to identify patients who would benefit most from a dissociative seizure-specific CBT approach. FUNDING: National Institute for Health Research, Health Technology Assessment programme

A Compact Multi-planet System with a Significantly Misaligned Ultra Short Period Planet

We report the discovery of a compact multi-planet system orbiting the relatively nearby (78 pc) and bright (K = 8.9) K-star, K2-266 (EPIC 248435473). We identify up to six possible planets orbiting K2-266 with estimated periods of P_b = 0.66, P_(.02) = 6.1, P_c = 7.8, P_d = 14.7, P_e = 19.5, and P_(.06) = 56.7 days, and radii of R_P = 3.3 R_⊕, 0.646 R_⊕, 0.705 R_⊕, 2.93 R_⊕, 2.73 R_⊕, and 0.90 R_⊕, respectively. We are able to confirm the planetary nature of two of these planets (d and e) by analyzing their transit timing variations ( (m_d = 8.9^(+5.7)_(−3.8) M_⊕ and m_e = 14.3^(+6.4)_(−5.0) M_⊕), confidently validate the planetary nature of two other planets (b and c), and classify the last two as planetary candidates (K2-266.02 and .06). From a simultaneous fit of all six possible planets, we find that K2-266 b's orbit has an inclination of 75fdg32 while the other five planets have inclinations of 87°–90°. This observed mutual misalignment may indicate that K2-266 b formed differently from the other planets in the system. The brightness of the host star and the relatively large size of the sub-Neptune sized planets d and e make them well-suited for atmospheric characterization efforts with facilities like the Hubble Space Telescope and upcoming James Webb Space Telescope. We also identify an 8.5 day transiting planet candidate orbiting EPIC 248435395, a co-moving companion to K2-266

The L 98-59 System: Three Transiting, Terrestrial-size Planets Orbiting a Nearby M Dwarf

We report the Transiting Exoplanet Survey Satellite (TESS) discovery of three terrestrial-size planets transiting L 98-59 (TOI-175, TIC 307210830)—a bright M dwarf at a distance of 10.6 pc. Using the Gaia-measured distance and broadband photometry, we find that the host star is an M3 dwarf. Combined with the TESS transits from three sectors, the corresponding stellar parameters yield planet radii ranging from 0.8 R ⊕ to 1.6 R ⊕. All three planets have short orbital periods, ranging from 2.25 to 7.45 days with the outer pair just wide of a 2:1 period resonance. Diagnostic tests produced by the TESS Data Validation Report and the vetting package DAVE rule out common false-positive sources. These analyses, along with dedicated follow-up and the multiplicity of the system, lend confidence that the observed signals are caused by planets transiting L 98-59 and are not associated with other sources in the field. The L 98-59 system is interesting for a number of reasons: the host star is bright (V = 11.7 mag, K = 7.1 mag) and the planets are prime targets for further follow-up observations including precision radial-velocity mass measurements and future transit spectroscopy with the James Webb Space Telescope; the near-resonant configuration makes the system a laboratory to study planetary system dynamical evolution; and three planets of relatively similar size in the same system present an opportunity to study terrestrial planets where other variables (age, metallicity, etc.) can be held constant. L 98-59 will be observed in four more TESS sectors, which will provide a wealth of information on the three currently known planets and have the potential to reveal additional planets in the system

Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

Telomere length is a risk factor in disease and the dynamics of telomere length are crucial to our understanding of cell replication and vitality. The proliferation of whole genome sequencing represents an unprecedented opportunity to glean new insights into telomere biology on a previously unimaginable scale. To this end, a number of approaches for estimating telomere length from whole-genome sequencing data have been proposed. Here we present Telomerecat, a novel approach to the estimation of telomere length. Previous methods have been dependent on the number of telomeres present in a cell being known, which may be problematic when analysing aneuploid cancer data and non-human samples. Telomerecat is designed to be agnostic to the number of telomeres present, making it suited for the purpose of estimating telomere length in cancer studies. Telomerecat also accounts for interstitial telomeric reads and presents a novel approach to dealing with sequencing errors. We show that Telomerecat performs well at telomere length estimation when compared to leading experimental and computational methods. Furthermore, we show that it detects expected patterns in longitudinal data, repeated measurements, and cross-species comparisons. We also apply the method to a cancer cell data, uncovering an interesting relationship with the underlying telomerase genotype