Integration of Data from Liquid–Liquid Phase Separation Databases Highlights Concentration and Dosage Sensitivity of LLPS Drivers

Liquid–liquid phase separation (LLPS) is a molecular process that leads to the formation of membraneless organelles, representing functionally specialized liquid-like cellular condensates formed by proteins and nucleic acids. Integrating the data on LLPS-associated proteins from dedicated databases revealed only modest agreement between them and yielded a high-confidence dataset of 89 human LLPS drivers. Analysis of the supporting evidence for our dataset uncovered a systematic and potentially concerning difference between protein concentrations used in a good fraction of the in vitro LLPS experiments, a key parameter that governs the phase behavior, and the proteomics-derived cellular abundance levels of the corresponding proteins. Closer scrutiny of the underlying experimental data enabled us to offer a sound rationale for this systematic difference, which draws on our current understanding of the cellular organization of the proteome and the LLPS process. In support of this rationale, we find that genes coding for our human LLPS drivers tend to be dosage-sensitive, suggesting that their cellular availability is tightly regulated to preserve their functional role in direct or indirect relation to condensate formation. Our analysis offers guideposts for increasing agreement between in vitro and in vivo studies, probing the roles of proteins in LLPS.     

Genes Involved in the Endoplasmic Reticulum N-Glycosylation Pathway of the Red Microalga Porphyridium sp.: A Bioinformatic Study

N-glycosylation is one of the most important post-translational modifications that influence protein polymorphism, including protein structures and their functions. Although this important biological process has been extensively studied in mammals, only limited knowledge exists regarding glycosylation in algae. The current research is focused on the red microalga Porphyridium sp., which is a potentially valuable source for various applications, such as skin therapy, food, and pharmaceuticals. The enzymes involved in the biosynthesis and processing of N-glycans remain undefined in this species, and the mechanism(s) of their genetic regulation is completely unknown. In this study, we describe our pioneering attempt to understand the endoplasmic reticulum N-Glycosylation pathway in Porphyridium sp., using a bioinformatic approach. Homology searches, based on sequence similarities with genes encoding proteins involved in the ER N-glycosylation pathway (including their conserved parts) were conducted using the TBLASTN function on the algae DNA scaffold contigs database. This approach led to the identification of 24 encoded-genes implicated with the ER N-glycosylation pathway in Porphyridium sp. Homologs were found for almost all known N-glycosylation protein sequences in the ER pathway of Porphyridium sp.; thus, suggesting that the ER-pathway is conserved; as it is in other organisms (animals, plants, yeasts, etc.).     

Gaucher Disease Diagnosis Using Lyso-Gb1 on Dry Blood Spot Samples: Time to Change the Paradigm?

For years, the gold standard for diagnosing Gaucher disease (GD) has been detecting reduced β-glucocerebrosidase (GCase) activity in peripheral blood cells combined with GBA1 mutation analysis. The use of dried blood spot (DBS) specimens offers many advantages, including easy collection, the need for a small amount of blood, and simpler transportation. However, DBS has limitations for measuring GCase activity. In this paper, we recount our cross-sectional study and publish seven years of experience using DBS samples and levels of the deacylated form of glucocerebroside, glucosylsphingosine (lyso-Gb1), for GD diagnosis. Of 444 screened subjects, 99 (22.3%) were diagnosed with GD at a median (range) age of 21 (1–78) years. Lyso-Gb levels for genetically confirmed GD patients vs. subjects negative to GD diagnosis were 252 (9–1340) ng/mL and 5.4 (1.5–16) ng/mL, respectively. Patients diagnosed with GD1 and mild GBA1 variants had lower median (range) lyso-Gb1, 194 (9–1050), compared to GD1 and severe GBA1 variants, 447 (38–1340) ng/mL, and neuronopathic GD, 325 (116–1270) ng/mL (p = 0.001). Subjects with heterozygous GBA1 variants (carrier) had higher lyso-Gb1 levels, 5.8 (2.5–15.3) ng/mL, compared to wild-type GBA1, 4.9 (1.5–16), ng/mL (p = 0.001). Lyso-Gb1 levels, median (range), were 5 (2.7–10.7) in heterozygous GBA1 carriers with Parkinson’s disease (PD), similar to lyso-Gb1 levels in subjects without PD. We call for a paradigm change for the diagnosis of GD based on lyso-Gb1 measurements and confirmatory GBA1 mutation analyses in DBS. Lyso-Gb1 levels could not be used to differentiate between heterozygous GBA1 carriers and wild type.     

Genetic Associations of Alcohol Dehydrogenase With Alcohol Use Disorders and Endophenotypes in White College Students.

Associations of alcohol dehydrogenase (ADH) gene polymorphisms (ADH1B*2 and ADH1C*1) with a lifetime alcohol use disorder (AUD) were examined in White college students. Alcohol-related endophenotypes likely to be influenced by elevations in acetaldehyde were also assessed. Individuals with an ADH1B*2 allele had lower rates of AUDs, consumed a lower maximum number of drinks in a 24-hr period, reported a greater level of response to alcohol, were more likely to have experienced alcohol-induced headaches following 1 or 2 drinks, and reported more severe hangovers than those lacking this allele. These findings are consistent with the hypothesis that enhanced sensitivity to alcohol and lower levels of alcohol use reflect the mechanism by which ADH1B*2 protects against developing an AUD. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Bacteriophages as viral pollution indicators

f2 Phage, attenuated Polio I (LSC) strain introduced daily to a 350 l. experimental oxidation pond showed no decrease in bacterial viruses f2 or other coliphages or Polio I strain.Ratios of coliphages to human enteric viruses ranged in flood waters from concentrations as low as 1:1 to as high as 10³:1; in wastewater at various seasons the ratio was 10⁵:1; in trickling filter effluents in winter it was 10⁴:1; in spring 10⁵:1, in summer and fall 10⁴:1, in oxidation pond effluents in winter 10³:1; in spring 10⁴:1; and in summer and fall 10³:1. Out of three epidemics in small communities caused by failure of water supply, coliphages were found to be positive. At the same time only two samples of human enteric viruses were positive (the third was contaminated with yeasts).Chlorination experiments using the experimental oxidation pond showed that f2 was most resistant, MS₂ was very resistant, and coliphages were more resistant than attenuated Polio I virus. Experiments with the oxidation pond effluents showed that coliphages were at least as or even more resistant to chlorine than human enteric viruses.     

Extraction of lipid-soluble antioxidants from rosemary leaves using vegetable oils

The objective of this research was to extract carnosic acid and carnosol, natural lipid-soluble antioxidants, from rosemary leaves without the use of chemical aid. Three different vegetable oils [high oleic soybean oil (HOSO), peanut oil (PO) and cottonseed oil (CO)] were used as the medium for extracting rosemary's lipid-soluble antioxidants. Dried rosemary leaves were ground into fine particles, added two of the selected vegetable oils, mixed and heated. The vegetable oil containing the extracted antioxidants was filtered from the rosemary particles and analysed using high-performance liquid chromatography (HPLC). As a control, a common extraction method using ethanol was performed to compare the oil extraction efficiency for carnosic acid and carnosol. HPLC analysis confirmed the presence of carnosic acid and carnosol in all three vegetable oil solutions. Compared to the ethanol extraction, a higher level of the carnosic acid was found in the vegetable oil solutions. Among the vegetable oils, high oleic soybean oil contained the most carnosic acid; however, there were similar amounts of carnosol in all three vegetable oil solutions. The extractions' efficacy was tested on soybean oil's (SO) oxidative stability by adding 2% (w/w) of the antioxidant–vegetable oil solution. The results obtained from peroxide value (PV) and p-anisidine value (AnV) analysis documented a significantly lower degree of oxidation in the soybean oil containing the extracted antioxidant solutions, compared to the pure soybean oil.     

Modelling the polypeptide backbone with 'spare parts' from known protein structures

An automatic procedure for building a protein polyalanine backbonefrom C positions and ‘spare parts’ retrieved froma data base of 66 high-resolution protein structures is described.Protein backbones are constructed from over-lapping fragmentsof variable length, which allows the backbone of regular secondarystructure elements to be built in one block. The procedure isshown to yield backbones which compare very favourably withthose from highly refined X-ray structures (r.m.s. deviationbetween generated and crystal structures <lÅ). Themethod is furthermore quite insensitive to experimental errorsin C positions as well as to the size of the data base, andis seen to yield valuable insight into the relationships betweensequence and 3-D structure: one example on triose phosphateisomerase, a ß-barrel protein, shows that ßloops can be considered as structurally more uncommon than ßloops. The ‘spare parts’ approach is also foundto be useful for general-purpose modelling of local structuralchanges produced by insertion or deletion of residues. It should,however, be used with caution. Crude selection criteria basedsolely on fragment length and geometric fit to the loop baseregions yield realistic backbones in about two-thirds of thetest cases (r.m.s. deviations from refined crystal structure{small tilde}lÅ). In the remaining cases, sequence information,in particular the presence of glycine residues which tend toadopt more unusual backbone conformations, must be consideredto obtain comparable results.     

A Comprehensive Assessment of Qualitative and Quantitative Prodromal Parkinsonian Features in Carriers of Gaucher Disease—Identifying Those at the Greatest Risk

Carriers of GBA1 gene variants have a significant risk of developing Parkinson’s disease (PD). A cohort study of GBA carriers between 40–75 years of age was initiated to study the presence of prodromal PD features. Participants underwent non-invasive tests to assess different domains of PD. Ninety-eight unrelated GBA carriers were enrolled (43 males) at a median age (range) of 51 (40–74) years; 71 carried the N370S variant (c.1226A > G) and 25 had a positive family history of PD. The Montreal Cognitive Assessment (MoCA) was the most frequently abnormal (23.7%, 95% CI 15.7–33.4%), followed by the ultrasound hyperechogenicity (22%, 95% CI 14–32%), Unified Parkinson’s Disease Rating Scale part III (UPDRS-III) (17.2%, 95% CI 10.2–26.4%), smell assessment (12.4%, 95% CI 6.6–20.6%) and abnormalities in sleep questionnaires (11%, 95% CI 5.7–19.4%). Significant correlations were found between tests from different domains. To define the risk for PD, we assessed the bottom 10th percentile of each prodromal test, defining this level as “abnormal”. Then we calculated the percentage of “abnormal” tests for each subject; the median (range) was 4.55 (0–43.5%). Twenty-two subjects had more than 15% “abnormal” tests. The limitations of the study included ascertainment bias of individuals with GBA-related PD in relatives, some incomplete data due to technical issues, and a lack of well-characterized normal value ranges in some tests. We plan to enroll additional participants and conduct longitudinal follow-up assessments to build a model for identifying individuals at risk for PD and investigate interventions aiming to delay the onset or perhaps to prevent full-blown PD.     

A window on the Israeli patent scene

In the last 15–20 years Israel has turned into a beehive of innovation and entrepreneurship. This article focuses on what was achieved and how the Information Professional can find and monitor these innovations. The main areas of innovation in Israel are high-tech, biotechnology, medical devices, irrigation, etc. Other topics are the role of start-ups and venture capital, IP strategy of Israeli companies, the Israeli Patents, Designs and Trademarks Office, how Israeli patents are published and how to obtain Israeli patents and documents.