Memory Upgrade: Insights into Primed Adaptation by CRISPR-Cas Immune Systems.

Recently, Künne et al. (2016) demonstrated that degradation products of Cas3 obtained during CRISPR interference fuel priming. In this issue of Molecular Cell, Xue et al. (2016) highlight the conformational changes in Cascade that underpin the priming process when interference is blocked.

Processing and integration of functionally oriented prespacers in the Escherichia coli CRISPR system depends on bacterial host exonucleases.

CRISPR-Cas systems provide bacteria with adaptive immunity against viruses. During spacer adaptation, the Cas1-Cas2 complex selects fragments of foreign DNA, called prespacers, and integrates them into CRISPR arrays in an orientation that provides functional immunity. Cas4 is involved in both the trimming of prespacers and the cleavage of protospacer adjacent motif (PAM) in several type I CRISPR-Cas systems, but how the prespacers are processed in systems lacking Cas4, such as the type I-E and I-F systems, is not understood. In Escherichia coli, which has a type I-E system, Cas1-Cas2 preferentially selects prespacers with 3' overhangs via specific recognition of a PAM, but how these prespacers are integrated in a functional orientation in the absence of Cas4 is not known. Using a biochemical approach with purified proteins, as well as integration, prespacer protection, sequencing, and quantitative PCR assays, we show here that the bacterial 3'-5' exonucleases DnaQ and ExoT can trim long 3' overhangs of prespacers and promote integration in the correct orientation. We found that trimming by these exonucleases results in an asymmetric intermediate, because Cas1-Cas2 protects the PAM sequence, which helps to define spacer orientation. Our findings implicate the E. coli host 3'-5' exonucleases DnaQ and ExoT in spacer adaptation and reveal a mechanism by which spacer orientation is defined in E. coli.

Characterization and Structural Insights into Selective E1-E2 Interactions in the Human and Plasmodium falciparum SUMO Conjugation Systems.

Protein modification by small ubiquitin-related modifiers (SUMOs) is essential and conserved in the malaria parasite, Plasmodium falciparum. We have previously shown that interactions between the SUMO E1-activating and E2-conjugating enzyme in P. falciparum are distinct compared with human, suggesting a potential target for development of parasite-specific inhibitors of SUMOylation. The parasite asexual trophozoite stage is susceptible to iron-induced oxidative stress and is subsequently a target for many of the current anti-malarial drugs. Here, we provide evidence that SUMOylation plays a role in the parasite response to oxidative stress during red blood cell stages, indicative of a protective role seen in other organisms. Using x-ray crystallography, we solved the structure of the human SUMO E1 ubiquitin fold domain in complex with the E2, Ubc9. The interface defined in this structure guided in silico modeling, mutagenesis, and in vitro biochemical studies of the P. falciparum SUMO E1 and E2 enzymes, resulting in the identification of surface residues that explain species-specific interactions. Our findings suggest that parasite-specific inhibitors of SUMOylation could be developed and used in combination therapies with drugs that induce oxidative stress.

A Survey on Recent Advances in Machine Learning Based Sleep Apnea Detection Systems.

Sleep apnea is a sleep disorder that affects a large population. This disorder can cause or augment the exposure to cardiovascular dysfunction, stroke, diabetes, and poor productivity. The polysomnography (PSG) test, which is the gold standard for sleep apnea detection, is expensive, inconvenient, and unavailable to the population at large. This calls for more friendly and accessible solutions for diagnosing sleep apnea. In this paper, we examine how sleep apnea is detected clinically, and how a combination of advances in embedded systems and machine learning can help make its diagnosis easier, more affordable, and accessible. We present the relevance of machine learning in sleep apnea detection, and a study of the recent advances in the aforementioned area. The review covers research based on machine learning, deep learning, and sensor fusion, and focuses on the following facets of sleep apnea detection: (i) type of sensors used for data collection, (ii) feature engineering approaches applied on the data (iii) classifiers used for sleep apnea detection/classification. We also analyze the challenges in the design of sleep apnea detection systems, based on the literature survey.

A Survey on Recent Advances in Wearable Fall Detection Systems.

With advances in medicine and healthcare systems, the average life expectancy of human beings has increased to more than 80 yrs. As a result, the demographic old-age dependency ratio (people aged 65 or above relative to those aged 15-64) is expected to increase, by 2060, from ∼28% to ∼50% in the European Union and from ∼33% to ∼45% in Asia (Ageing Report European Economy, 2015). Therefore, the percentage of people who need additional care is also expected to increase. For instance, per studies conducted by the National Program for Health Care of the Elderly (NPHCE), elderly population in India will increase to 12% of the national population by 2025 with 8%-10% requiring utmost care. Geriatric healthcare has gained a lot of prominence in recent years, with specific focus on fall detection systems (FDSs) because of their impact on public lives. According to a World Health Organization report, the frequency of falls increases with increase in age and frailty. Older people living in nursing homes fall more often than those living in the community and 40% of them experience recurrent falls (World Health Organization, 2007). Machine learning (ML) has found its application in geriatric healthcare systems, especially in FDSs. In this paper, we examine the requirements of a typical FDS. Then we present a survey of the recent work in the area of fall detection systems, with focus on the application of machine learning. We also analyze the challenges in FDS systems based on the literature survey.

Cardioprotective potential of polyphenols rich Thraatchathi Chooranam against isoproterenol induced myocardial necrosis in experimental rats.

BACKGROUND: The present study establishes the cardioprotective role of Thraatchathi Chooranam (TC), a polyherbal traditional Siddha medicine, in terms of membrane stabilizing and antioxidant properties in isoproterenol (ISO) induced myocardial necrosis model in rats. METHODS: Animals were divided into six groups (n = 6), normal (received vehicle 0.5% CMC, p.o.), ISO control (received 0.5% CMC + ISO 120 mg/kg, b.w. s.c. twice at an interval of 48 h), standard control (received Vit-E 100 mg/kg, p.o.) + ISO, TC low and high dose (50 and 100 mg/kg p.o., respectively) + ISO, and drug control (received TC at 100 mg/kg, p.o.). At the end of experimental period, blood samples collected and plasma cardiac troponin-I (CTn-I) was measured by ELISA. Cardiac tissues were isolated, levels of membrane stabilizing enzymes, antioxidants and inflammatory markers were estimated. Gene expression of Bax, Bcl2, Caspase 3, HIF-α, TNF-α, iNOS, TRX1 and TrxR were performed by RT-PCR. Histopathological studies on cardiac tissues were conducted using hematoxylin and eosin (H&E) stain. Statistical analyses were performed by one-way ANOVA followed by Tukey's multiple comparison as post-hoc test. RESULTS: Administration of ISO resulted in a significant increase in plasma CTn-I, decrease in superoxide dismutase, glutathione and glutathione peroxidase; it also significantly altered membrane stabilizing enzymes like Na+/K+-ATPase, Mg2+-ATPase Ca2+-ATPase and Cathepsin D. Pretreatment with TC (50 mg/kg and 100 mg/kg) decreased CTn-I, and improved membrane stabilizing and endogenous antioxidant enzymes and decreased cathespin D level in a dose dependent manner. Histopathological examination revealed that TC improves cellular membrane integrity and decreases inflammatory cell infiltration and necrotic death. CONCLUSION: The present study provided a strong evidence on the protective effects of TC against ISO-induced myocardial necrosis in rats.

Transmitted HIV drug resistance among HIV-infected voluntary counseling and testing centers (VCTC) clients in Mumbai, India.

A survey for transmitted HIV drug resistance (HIVDR) was conducted according to WHO guidelines among clients newly diagnosed with HIV-1 infection at two voluntary counseling and testing centers (VCTC) in Mumbai. HIVDR testing was performed using the ViroSeq RT-PCR method (Abbott). Out of 50 successfully amplified and sequenced specimens, analysis of the first 34 consecutively collected specimens revealed no nucleoside reverse transcriptase inhibitor, nonnucleoside reverse transcriptase inhibitor, or protease inhibitor mutations from the 2007 WHO list of mutations for surveillance of transmitted HIVDR, indicating that the prevalence of transmitted HIVDR to all three drug classes was <5% among recently infected VCTC clients in Mumbai. The phylogenetic analysis revealed that all samples belonged to HIV-1 subtype C. Continued ART program monitoring and further evaluation of transmitted HIV drug resistance in coming years are essential in Mumbai as well as in other regions of the country in which ART is being scaled up rapidly.