A User’s Guide for Phase Separation Assays with Purified Proteins

The formation of membrane-less organelles and compartments by protein phase separation is an important way in which cells organize their cytoplasm and nucleoplasm. In vitro phase separation assays with purified proteins have become the standard way to investigate proteins that form membrane-less compartments. By now, various proteins have been purified and tested for their ability to phase separate and form liquid condensates in vitro. However, phase-separating proteins are often aggregation-prone and difficult to purify and handle. As a consequence, the results from phase separation assays often differ between labs and are not easily reproduced. Thus, there is an urgent need for high-quality proteins, standardized procedures, and generally agreed-upon practices for protein purification and conducting phase separation assays. This paper provides protocols for protein purification and guides the user through the practicalities of in vitro protein phase separation assays, including best-practice approaches and pitfalls to avoid. We believe that this compendium of protocols and practices will provide a useful resource for scientists studying the phase behavior of proteins.     

A Beginner’s Guide to Phylogenetics

Metagenomics and the development of high throughput next generation sequencing capabilities have forced significant development in the field of phylogenetics: the study of the evolutionary relatedness of the planet’s inhabitants. Herein, I review the major tree-building strategies, challenges and opportunities which exist in this rapidly expanding field of evolutionary biology.     

The AlphaFold Database of Protein Structures: A Biologist’s Guide

AlphaFold, the deep learning algorithm developed by DeepMind, recently released the three-dimensional models of the whole human proteome to the scientific community. Here we discuss the advantages, limitations and the still unsolved challenges of the AlphaFold models from the perspective of a biologist, who may not be an expert in structural biology.     

Women’s Perceptions and Misperceptions of Male Circumcision: A Mixed Methods Study in Zambia

Women’s perceptions of male circumcision (MC) have implications for behavioral risk compensation, demand, and the impact of MC programs on women’s health. This mixed methods study combines data from the first two rounds of a longitudinal study (n = 934) and in-depth interviews with a subsample of respondents (n = 45) between rounds. Most women correctly reported that MC reduces men’s risk of HIV (64% R1, 82% R2). However, 30% of women at R1, and significantly more (41%) at R2, incorrectly believed MC is fully protective for men against HIV. Women also greatly overestimated the protection MC offers against STIs. The proportion of women who believed MC reduces a woman’s HIV risk if she has sex with a man who is circumcised increased significantly (50% to 70%). Qualitative data elaborate women’s misperception regarding MC. Programs should address women’s informational needs and continue to emphasize that condoms remain critical, regardless of male partner’s circumcision status.     

A Mouse Geneticist’s Practical Guide to CRISPR Applications

CRISPR/Cas9 system of RNA-guided genome editing is revolutionizing genetics research in a wide spectrum of organisms. Even for the laboratory mouse, a model that has thrived under the benefits of embryonic stem (ES) cell knockout capabilities for nearly three decades, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 technology enables one to manipulate the genome with unprecedented simplicity and speed. It allows generation of null, conditional, precisely mutated, reporter, or tagged alleles in mice. Moreover, it holds promise for other applications beyond genome editing. The crux of this system is the efficient and targeted introduction of DNA breaks that are repaired by any of several pathways in a predictable but not entirely controllable manner. Thus, further optimizations and improvements are being developed. Here, we summarize current applications and provide a practical guide to use the CRISPR/Cas9 system for mouse mutagenesis, based on published reports and our own experiences. We discuss critical points and suggest technical improvements to increase efficiency of RNA-guided genome editing in mouse embryos and address practical problems such as mosaicism in founders, which complicates genotyping and phenotyping. We describe a next-generation sequencing strategy for simultaneous characterization of on- and off-target editing in mice derived from multiple CRISPR experiments. Additionally, we report evidence that elevated frequency of precise, homology-directed editing can be achieved by transient inhibition of the Ligase IV-dependent nonhomologous end-joining pathway in one-celled mouse embryos.     

Nutritional,antimicrobial and medicinal properties of Camel’s milk: A review

Camel’s milk is an important part of staple diet in several parts of the world, particularly in the arid and semi-arid zones. Camel’s milk is rich in health-beneficial substances, such as bioactive peptides, lactoferrin, zinc, and mono and polyunsaturated fatty acids. These substances could help in the treatment of some important human diseases like tuberculosis, asthma, gastrointestinal diseases, and jaundice. Camel’s milk composition is more variable compared to cow’s milk. The effects of feed, breed, age, and lactation stage on milk composition are more significant in camel. Region and season significantly change the ratio of compounds in camel’s milk. Camel’s whey protein is not only composed of numerous soluble proteins, but also has indigenous proteases such as chymotrypsin A and cathepsin D. In addition to their high nutritional value, these whey proteins have unique characteristics, including physical, chemical, physiological, functional, and technological features that are useful in the food application. The hydrolysis of camel’s milk proteins leads to the formation of bioactive peptides, which affect major organ systems of the body and impart physiological functions to these systems. The camel’s milk has antioxidant, antimicrobial, angiotensin-I-converting enzyme (ACE)-inhibitory peptides, antidiabetic as well as anticholesterol activities.     

The State of Ethnoprimatology: Its Use and Potential in Today’s Primate Research

The human–primate interface is an increasingly relevant theme in primatological research. To understand the extent of ethoprimatological studies in contemporary primatology, we explored 7 years of primatological literature through a systematic review. We reviewed original research papers published in the American Journal of Primatology, the International Journal of Primatology, Primates, and Folia Primatologica between January 2010 and December 2016 for the presence of 14 search terms relevant to the ethnoprimatological approach. We sorted research papers into topical categories to identify trends in the recent primatological literature. Of the 1551 papers that met the criteria for inclusion in this review, 12 papers (0.8%) self-identified as an ethnoprimatological study by using the term in the title or keywords, and only 17 papers (1.1%) used the term anywhere in their text. However, the presence of other relevant keywords—anthropogenic (16.3%), crop (9.1%), disturbance (18.7%), conflict (6.2%), human–nonhuman (0.5%), human–primate (1.0%), interface (1.5%), perception (2.5%), culture (2.6%), ethnography (0.1%), trade (6.8%), provision (16.1%), and tourism (4.6%)—in a variety of research papers suggests that the human–primate dimension is salient for many, if not most, areas of primatological interest. The ethnoprimatological approach is relevant to every research trend we identified in today’s primatology. We highlight existing literature that exemplifies ethnoprimatological engagement and present potential research questions in each area, demonstrating that primatology as a whole would benefit from greater attention to the human dimension.     

The Hitchhiker’s Guide to Nucleocytoplasmic Trafficking in Neurodegeneration

Neurochemical Research - The widespread nature of nucleocytoplasmic trafficking defects and protein accumulation suggests distinct yet overlapping mechanisms in a variety of neurodegenerative...     

A Mathematical Biologist’s Guide to Absolute and Convective Instability

Mathematical models have been highly successful at reproducing the complex spatiotemporal phenomena seen in many biological systems. However, the ability to numerically simulate such phenomena currently far outstrips detailed mathematical understanding. This paper reviews the theory of absolute and convective instability, which has the potential to redress this inbalance in some cases. In spatiotemporal systems, unstable steady states subdivide into two categories. Those that are absolutely unstable are not relevant in applications except as generators of spatial or spatiotemporal patterns, but convectively unstable steady states can occur as persistent features of solutions. The authors explain the concepts of absolute and convective instability, and also the related concepts of remnant and transient instability. They give examples of their use in explaining qualitative transitions in solution behaviour. They then describe how to distinguish different types of instability, focussing on the relatively new approach of the absolute spectrum. They also discuss the use of the theory for making quantitative predictions on how spatiotemporal solutions change with model parameters. The discussion is illustrated throughout by numerical simulations of a model for river-based predator–prey systems.     

Autophagy: A double-edged sword in Alzheimer’s disease

Autophagy is a major protein degradation pathway that is essential for stress-induced and constitutive protein turnover. Accumulated evidence has demonstrated that amyloid-beta (A beta) protein can be generated in autophagic vacuoles, promoting its extracellular deposition in neuritic plaques as the pathological hallmark of Alzheimer's disease (AD). The molecular machinery for A beta generation, including APP, APP-C99 and beta-/gamma-secretases, are all enriched in autophagic vacuoles. The induction of autophagy can be vividly observed in the brain at early stages of sporadic AD and in an AD transgenic mouse model. Accumulated evidence has also demonstrated a neuroprotective role of autophagy in mediating the degradation of aggregated proteins that are causative of various neurodegenerative diseases. Autophagy is thus widely regarded as an intracellular hub for the removal of the detrimental A beta peptides and Tau aggregates. Nonetheless, compelling data also reveal an unfavorable function of autophagy in facilitating the production of intracellular A beta. The two faces of autophagy on the homeostasis of A beta place it in a very unique and intriguing position in AD pathogenesis. This article briefly summarizes seminal discoveries that are shedding new light on the critical and unique roles of autophagy in AD and potential therapeutic approaches against autophagy-elicited AD.     

Daytime Sleepiness in Parkinson’s Disease: A Reappraisal

Background

Excessive daytime sleepiness is a frequent complaint in Parkinson’s disease (PD); however the frequency and risk factors for objective sleepiness remain mostly unknown. We investigated both the frequency and determinants of self-reported and objective daytime sleepiness in patients with Parkinson’s disease (PD) using a wide range of potential predictors.

Methods

One hundred and thirty four consecutive patients with PD, without selection bias for sleep complaint, underwent a semi-structured clinical interview and a one night polysomnography followed by a multiple sleep latency test (MSLT). Demographic characteristics, medical history, PD course and severity, daytime sleepiness, depressive and insomnia symptoms, treatment intake, pain, restless legs syndrome, REM sleep behaviour disorder, and nighttime sleep measures were collected. Self-reported daytime sleepiness was defined by an Epworth Sleepiness Scale (ESS) score above 10. A mean sleep latency on MSLT below 8 minutes defined objective daytime sleepiness.

Results

Of 134 patients with PD, 46.3% had subjective and only 13.4% had objective sleepiness with a weak negative correlation between ESS and MSLT latency. A high body mass index (BMI) was associated with both ESS and MSLT, a pain complaint with ESS, and a higher apnea/hypopnea index with MSLT. However, no associations were found between both objective and subjective sleepiness, and measures of motor disability, disease onset, medication (type and dose), depression, insomnia, restless legs syndrome, REM sleep behaviour disorder and nighttime sleep evaluation.

Conclusion

We found a high frequency of self-reported EDS in PD, a finding which is however not confirmed by the gold standard neurophysiological evaluation. Current treatment options for EDS in PD are very limited; it thus remains to be determined whether decreasing pain and BMI in association with the treatment of sleep apnea syndrome would decrease significantly daytime sleepiness in PD.     

Icariin: A Potential Neuroprotective Agent in Alzheimer’s Disease and Parkinson’s Disease

Alzheimer’s disease (AD) and Parkinson’s disease (PD) are the most common neurodegenerative diseases worldwide. They are characterized by the loss of neurons and synapses in special parts of the central nervous system (CNS). There is no definitive treatment for AD and PD, but extensive studies are underway to identify the effective drugs which can slow the progression of these diseases by affecting the factors involved in their pathophysiology (i.e., aggregated proteins, neuroinflammation, and oxidative stress). Icariin, a natural compound isolated from Epimedii herba, is known because of its anti-inflammatory and anti-oxidant properties. In this regard, there are numerous studies indicating its potential as a natural compound against the progression of CNS disorders, such as neurodegenerative diseases. Therefore, this review aims to re-examine findings on the pharmacologic effects of icariin on factors involved in the pathophysiology of AD and PD.

     

Parkinson’s Disease in Saudi Patients: A Genetic Study

Parkinson’s disease (PD) is one of the major causes of parkinsonism syndrome. Its characteristic motor symptoms are attributable to dopaminergic neurons loss in the midbrain. Genetic advances have highlighted underlying molecular mechanisms and provided clues to potential therapies. However, most of the studies focusing on the genetic component of PD have been performed on American, European and Asian populations, whereas Arab populations (excluding North African Arabs), particularly Saudis remain to be explored. Here we investigated the genetic causes of PD in Saudis by recruiting 98 PD-cases (sporadic and familial) and screening them for potential pathogenic mutations in PD-established genes; SNCA, PARKIN, PINK1, PARK7/DJ1, LRRK2 and other PD-associated genes using direct sequencing. To our surprise, the screening revealed only three pathogenic point mutations; two in PINK1 and one in PARKIN. In addition to mutational analysis, CNV and cDNA analysis was performed on a subset of patients. Exon/intron dosage alterations in PARKIN were detected and confirmed in 2 cases. Our study suggests that mutations in the ORF of the screened genes are not a common cause of PD in Saudi population; however, these findings by no means exclude the possibility that other genetic events such as gene expression/dosage alteration may be more common nor does it eliminate the possibility of the involvement of novel genes.     

Audrey’s Overhang: A Pictographic Maze in Central Montana

Abstract

Audrey’s Overhang, a small pictograph site in Montana’s Smith River Drainage, is part of a highly abstract rock art style localized in the Rocky Mountain foothills of central Montana. An abstract anthropomorph at Audrey’s Overhang is similar to those at several nearby sites. Site characteristics suggest that the pictographs of this rock art style were painted as part of a vision guest ceremony. Because the rock art of much of the surrounding area is poorly known the external relationships of this central Montana rock art style remain to be demonstrated.     

Optical Coherence Tomography in Alzheimer’s Disease: A Meta-Analysis

Background

Alzheimer’s disease (AD) is a neurodegenerative disorder, which is likely to start as mild cognitive impairment (MCI) several years before the its full-blown clinical manifestation. Optical coherence tomography (OCT) has been used to detect a loss in peripapillary retina nerve fiber layer (RNFL) and a reduction in macular thickness and volume of people affected by MCI or AD. Here, we performed an aggregate meta-analysis combining results from different studies.

Methods and Findings

Data sources were case-control studies published between January 2001 and August 2014 (identified through PubMed and Google Scholar databases) that examined the RNFL thickness by means of OCT in AD and MCI patients compared with cognitively healthy controls.

Results

11 studies were identified, including 380 patients with AD, 68 with MCI and 293 healthy controls (HC). The studies suggest that the mean RNFL thickness is reduced in MCI (weighted mean differences in μm, WMD = -13.39, 95% CI: -17.34 to -9.45, p = 0.031) and, even more so, in AD (WMD = -15.95, 95% CI: -21.65 to -10.21, p<0.0001) patients compared to HC. RNFL in the 4 quadrants were all significantly thinner in AD superior (superior WMD = -24.0, 95% CI: -34.9 to -13.1, p<0.0001; inferior WMD = -20.8, 95% CI: -32.0 to -9.7, p<0.0001; nasal WMD = -14.7, 95% CI: -23.9 to -5.5, p<0.0001; and temporal WMD = -10.7, 95% CI: -19.9 to -1.4, p<0.0001); the same significant reduction in quadrant RNFL was observed in MCI patients compared with HC (Inferior WMD = -20.22, 95% CI: -30.41 to -10.03, p = 0.0001; nasal WMD = -7.4, 95% CI: -10.08 to -4.7, p = 0.0000; and temporal WMD = -6.88, 95% CI: -12.62 to -1.13, p = 0.01), with the exception of superior quadrant (WMD = -19.45, 95% CI: -40.23 to 1.32, p = 0.06).

Conclusion

Results from the meta-analysis support the important role of OCT for RNFL analysis in monitoring the progression of AD and in assessing the effectiveness of purported AD treatments.