A practical overview of protein disorder prediction methods

In the past few years there has been a growing awareness that a large number of proteins contain long disordered (unstructured) regions that often play a functional role. However, these disordered regions are still poorly detected. Recognition of disordered regions in a protein is important for two main reasons: reducing bias in sequence similarity analysis by avoiding alignment of disordered regions against ordered ones, and helping to delineate boundaries of protein domains to guide structural and functional studies. As none of the available method for disorder prediction can be taken as fully reliable on its own, we present an overview of the methods currently employed highlighting their advantages and drawbacks. We show a few practical examples of how they can be combined to avoid pitfalls and to achieve more reliable predictions.     

Different Methods for Assessing the Features of Eating Disorders in Patients with Binge Eating Disorder: A Replication

Objective: To compare different methods for assessing the features of eating disorders in patients with binge eating disorder (BED). Research Methods and Procedures: A total of 47 participants with BED were administered the Eating Disorder Examination (EDE) Interview and completed the EDE‐Questionnaire (EDE‐Q) at baseline. A total of 37 participants prospectively self‐monitored their eating behaviors daily for 4 weeks and then completed another EDE‐Q. Results: At baseline, the EDE and the EDE‐Q were significantly correlated on frequencies of objective bulimic episodes (binge eating), overeating episodes, and on the dietary restraint, eating concern, weight concern, and shape concern subscales. Mean differences in the EDE and EDE‐Q frequencies of objective bulimic episodes and overeating were not significant but scores on the four subscales differed significantly, with the EDE‐Q yielding higher scores. At the 4‐week point, the EDE‐Q retrospective 28‐day assessment was significantly correlated with the prospective daily self‐monitoring records for frequency of objective bulimic episodes and the mean difference between the methods was not significant. The EDE‐Q and self‐monitoring findings for subjective bulimic episodes and objective overeating differed significantly. Discussion: In patients with BED, the three assessment methods showed some areas of acceptable convergence.     

Seasonal pattern in bipolar disorders and cardio-vascular risk factors: A study from the FACE-BD cohort

Seasonal pattern (SP) and metabolic syndrome (MetS) are major contributors to poor outcome in bipolar disorders (BD). Patients with seasonal bipolar depression present increased appetite, carbohydrate cravings, weight gain, and hypersomnia, which can increase the development of MetS. MetS also appears to be associated with seasonal mood changes in the general population. This study examines whether a SP in BD is associated with an increased risk of MetS and its sub-components. One thousand four hundred and seventy-one outpatients with BD were systematically enrolled from 2009 to 2016. Inclusion required a disease duration of at least 5 years, with 486 (33%) patients with SP (SP+) and 985 (67%) without (SP–) according to the DSM IV-TR criteria. When using continuous measures of metabolic components, SP+ patients, as compared to SP–, suffered from higher levels for systolic blood pressure (p = 0.01), low-density lipoprotein cholesterol (p = 0.009), fasting glucose (p = 0.007), triglycerides levels (p = 0.03), a larger abdominal circumference (p = 0.02), and a higher body mass index (p = 0.07). In the covariance analysis, adjusted for gender, age, and bipolar subtype, as well as the number of depressive and hypomanic episode, SP+ patients had a significantly higher level of fasting glucose and higher systolic blood pressure. The frequency of MetS did not differ between groups (21.2% in SP– versus 23.9% in SP+). When using categorical definitions for abnormal metabolic components (International Diabetes Federation criteria), there were no differences between groups, except that SP+ patients were more overweight/obese as compared to SP– patients (55.03% versus 46.7%, respectively; p = 0.002) and tended to have more frequently high fasting glucose (18.2% versus 14.3%, respectively; p = 0.07). MetS was frequent in patients with BD, however not associated with SP. Patients with SP appeared more vulnerable to overweight/obesity and presented with higher levels of MetS subcomponents although these parameters were mainly in the normal range. All patients with BD should benefit from early screening and targeted management of cardio-vascular risk factors.     

The CLOCK Gene and Mood Disorders: A Case-Control Study and Meta-analysis

The clock gene (CLOCK) is considered to be a good candidate gene for the pathophysiology of mood disorders, including bipolar disorder (BP) and major depressive disorder (MDD). rs1801260 (T3111C) has been detected at position 3111 in the CLOCK mRNA 3' untranslated region, and was reported to be associated with a substantial delay in preferred timing for activity and sleep in a human study. As for function, rs1801260 has been speculated to affect mRNA. Therefore, the authors investigated the association between the three tagging single-nucleotide polymorphisms (SNPs) (rs3736544, rs1801260, and rs3749474) in CLOCK and risk of BP (n?=?867) and MDD (n?=?139) compared to controls (n?=?889) in the Japanese population. In addition, we also performed an updated meta-analysis of nine published, genetic association studies investigating the relationship between rs1801260 and mood disorder risk, comprising 3321 mood disorders cases and 3574 controls. We did not detect any associations between tagging SNPs in CLOCK and BP or MDD in the allele, genotype, or haplotype analysis (global p_BP?=?.605 and global p_MDD?=?.211). Moreover, rs1801260 was also not associated with BP, MDD, or any mood disorders in the meta-analysis. In conclusion, these data suggest that CLOCK does not play a major role in the pathophysiology of mood disorders. (Author correspondence: tarok@fujita-hu.ac.jp)     

A CHIPotle in physiology and disease

The carboxy-terminus of Hsc70 interacting protein (CHIP) is known to function as a chaperone associated E3 ligase for several proteins and regulates a variety of physiological processes. Being a connecting link between molecular chaperones and 26S proteasomes, it is widely regarded as the central player in the cellular protein quality control system. Recent analyses have provided new insights on the biochemical and functional dynamics of CHIP. In this review article, we give a comprehensive account of our current knowledge on the biology of CHIP, which apart from shedding light on fundamental biological questions promises to provide a potential target for therapeutic intervention.     

A LONGITUDINAL INVESTIGATION OF SEASONAL VARIATION IN MOOD

A prospective panel study was conducted to measure seasonality of mood in a random community sample in Melbourne, Australia (N = 245). Based on research into the structure of human mood, it was predicted that a lowering of mood in winter relative to summer would be observed in positive affect (PA) and behavioral engagement (BE), but not negative affect (NA). These variables were measured across summer and winter for 3 years. Consistent with the majority of research in the Northern Hemisphere, analyses on the entire sample found evidence of a small prospective season effect on the BE scale (explaining 2.1% of variance in BE scores). Also, as expected, no season effect was seen on the NA scale. In the entire sample, the season effect was not significant for PA, but joint factor analysis of the BE, PA, and NA scales confirmed that the season effect seen in the BE scale was largely due to items that were pure measures of PA. Winter pattern seasonality was both reliable across measures and significantly more marked among the subgroup of respondents who self-identified winter pattern of mood on the Seasonal Pattern Assessment Questionnaire. (Chronobiology International, 18(5), 875-891, 2001)     

A proliferative disorder of possible hemic origin in the common cockle,Cerastoderma edule

A study is described concerning the infestation of a laboratory-reared Daphnia magna culture by the fungus Aphanomyces daphniae. The origin of this fungus is Lake Huron, Michigan, the water from which is used in the laboratory to culture daphnids and maintain fishes for toxicological testing. Infestations originate from the Lake during the autumnal and vernal homothermal periods. The fungus is apparently maintained in the laboratory in conjunction with the fishes. Onset of fungal infestations in zooplankton culture apparently is initiated by three types of stress: rising temperatures, declining dissolved oxygen values, and poor nutrition. These infections have been eliminated by separating the daphnid culturing facility from the fish facility, substituting an algal diet for a synthetic one, sterilizing all water, air, and glassware connected with zooplankton culture, and maintaining the daphnids in a constant temperature room with controlled dissolved oxygen levels in the culturing vessels.     

SLEEP-WAKE SCHEDULE DISORDER DISABILITY: A LIFELONG UNTREATABLE PATHOLOGY OF THE CIRCADIAN TIME STRUCTURE

Certain sleep-wake schedule disorders (SWSDs) cannot be successfully managed clinically using conventional methods of sleep therapy. We describe two cases of SWSD, the first following head trauma and the second originating during childhood, that had been misdiagnosed by physicians for many years. After conventional treatment for SWSD with light therapy and melatonin failed to bring about substantial improvement, it was determined that they were suffering from an incurable disability. Hence, we propose new medical terminology for such cases—SWSD disability. SWSD disability is an untreatable pathology of the circadian time structure. Patients suffering from SWSD disability should be encouraged to accept the fact that they suffer from a permanent disability, and that their quality of life can only be improved if they are willing to undergo rehabilitation. It is imperative that physicians recognize the medical condition of SWSD disability in their patients and bring it to the notice of the public institutions responsible for vocational and social rehabilitation. (Chronobiology International, 18(6), 1019–1027, 2001)     

SLEEP-WAKE SCHEDULE DISORDER DISABILITY: A LIFELONG UNTREATABLE PATHOLOGY OF THE CIRCADIAN TIME STRUCTURE

Certain sleep-wake schedule disorders (SWSDs) cannot be successfully managed clinically using conventional methods of sleep therapy. We describe two cases of SWSD, the first following head trauma and the second originating during childhood, that had been misdiagnosed by physicians for many years. After conventional treatment for SWSD with light therapy and melatonin failed to bring about substantial improvement, it was determined that they were suffering from an incurable disability. Hence, we propose new medical terminology for such cases—SWSD disability. SWSD disability is an untreatable pathology of the circadian time structure. Patients suffering from SWSD disability should be encouraged to accept the fact that they suffer from a permanent disability, and that their quality of life can only be improved if they are willing to undergo rehabilitation. It is imperative that physicians recognize the medical condition of SWSD disability in their patients and bring it to the notice of the public institutions responsible for vocational and social rehabilitation. (Chronobiology International, 18(6), 1019-1027, 2001)     

Multiple conformations of amino acid residues in ribonuclease A

The highly refined 1.26 A structure (R = 0.15) of phosphate-free bovine pancreatic ribonuclease A was modeled with 13 residues having discrete multiple conformations of side chains. These residues are widely distributed over the protein surface, but only one of them, Lys 61, is involved in crystal packing interactions. The discrete conformers have no unusual torsion angles, and their interactions with the solvent and with other atoms of the protein are similar to those residues modeled with a single conformation. For three of the residues--Val 43, Asp 83, and Arg 85--two correlated conformations are found. The observed multiple conformations on the protein surfaces will be of significance in analyzing structure-function relationships and in performing protein engineering.     

采后菠萝黑心病诱导因素的研究

本文叙述了外源赤霉素ＧＡ３、低温条件对采后菠萝果实黑心病发展的影响．说明外源赤霉素ＧＡ３和低温条件都是诱导菠萝黑心病的重要因子。菠萝黑心病是一种生理失调症。实验中,未发现化学杀菌剂对此种病症显现出防治效果,而采后贮前４０℃高温处理２４小时．则可以减少和延迟此病的发生,因此．后者是一种可以应用于商品菠萝果实黑心病防治的好方法。     

Late-life Onset Bipolar Disorder Presenting as a Case of Pseudo-Dementia: A Case Discussion and Review of Literature

Depression and comorbid cognitive impairment in the elderly can be difficult to distinguish from dementia. Adding to the complex differential is that depression may be part of a bipolar illness rather than a unipolar mood disorder. A diligent workup and close monitoring of patients can inform appropriate treatment and can make the difference between recovery and persistence of symptoms. The present case will illustrate how a comprehensive workup utilizing extensive data gathering, laboratory workup, use of neuropsychological testing, neuroimaging, and timely treatment can lead to successful clinical outcomes that can be sustained for many years.     

Impact of polycystic ovary syndrome on eating behavior,depression and health related quality of life: A cross-sectional study in Riyadh

Background & objectivesPolycystic ovary syndrome (PCOS) is the most common endocrinal disorder, and the greatest cause of infertility in women. Despite availability of individual data on impact of multiple endocrinal, reproductive and even metabolic factors in PCOS individuals, the data on the co-existence of BED and depression in PCOS patients with its relationship on the quality of life in Saudi Arabian females is not found. Hence this study is aimed to elucidate the implication of PCOS on eating behaviour, induction of depression and general health quality in Saudi Arabian population of Riyadh.Materials and methodsThis is a cross-sectional study carried out in multiple health facilities of Riyadh from January to March 2019. The study samples (494) were recruited by convenience sampling and administered validated questionnaire by trained research participants. The data obtained was analysed by binary logistic regression using SPSS-IBM 25.ResultsOf the total 494 women participated in the study, 23.48% (116) were PCOS individuals. The odds of developing abnormal health related quality of (HRQ) in patients with PCOS was significantly (P = 0.000, OR = 3.472) high when compared to non-PCOS participants. The odds of showing high binge eating disorder (BED, P = 0.007, OR = 2.856) and depression (P = 0.000, OR = 2.497) scores in PCOS participants were significantly more than patients who were not having PCOS. Out of the three parameters studied, abnormal health related quality of life possessed a higher influence of PCOS compared to depression and abnormal eating behavior.Interpretation & conclusionIn conclusion, the present study shows that women with PCOS are at a significant risk for depressive disorders, disorganized eating behavior and impaired quality of life. Therefore, necessary care and screening is required to minimize the impact of PCOS on already burdened individuals.     

ProADD: A database on Protein Aggregation Diseases

ProADD, a database for protein aggregation diseases, is developed to organize the data under a single platform to facilitate easy access for researchers. Diseases caused due to protein aggregation and the proteins involved in each of these diseases are integrated. The database helps in classification of proteins involved in the protein aggregation diseases based on sequence and structural analysis. Analysis of proteins can be done to mine patterns prevailing among the aggregating proteins.

Availability

http://bicmku.in/ProADD     

Hemostatic profile detailing in apparent VWD cases: A cross sectional study

The von willebrand disease (vWD) accounts to be one of the most common hereditary bleeding ailment that amounts its incidence to almost 1.5% of normal population. It is mostly associated with a defect in primary hemostasis as well as secondary defect in coagulation factor VIII as diagnosis of vwd happened to be challenging with earlier diagnostic criteria’s. Testing Vwd in menorrhagia patients was not at ease. A cross-sectional study was conducted in female patients who have visited obstetrics and gynecology clinic at King Saud University Medical City (KSUMC), Riyadh, Saudi Arabia. The inclusion criteria consist of adult female patients between 16 and 45 years old with menorrhagia. A sample of 45 patients were screened and selected for the above-mentioned study. The SPSS Statistical analysis package was performed to analyze the data’s. The fisher’s exact test was conducted to compare the demographic variables. The independent samples t-test was conducted to compare the means of subjects. The P value of ≤0.05 considered as statistically significant. The cases manifested with a history of bleeding during periods stretching from 7 to 90 days. The vWD was reported in 6.6 % (n = 3) women out of the total 45 patients. The vWF: Ac mean ± SD (51.4 ± 6.3) and vWF: Ag Mean ± SD (93 ± 67) were significantly lesser in vWD patients with that of non-vWD (98.7 ± 22.6) vs (116 ± 42.4) (p = 0.027) (p = 0.032) respectively. WBC, ESR, MCV, MCH, Hemoglobin, PLT count, INR, PT, APTT and FVIII showed no significant difference among the groups (p > 0.05).