Autism genes: the continuum that connects us all

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Network Security Modelling with Distributional Data

We investigate the detection of botnet command and control (C2) hosts in massive IP traffic using machine learning methods. To this end, we use NetFlow data -- the industry standard for monitoring of IP traffic -- and ML models using two sets of features: conventional NetFlow variables and distributional features based on NetFlow variables. In addition to using static summaries of NetFlow features, we use quantiles of their IP-level distributions as input features in predictive models to predict whether an IP belongs to known botnet families. These models are used to develop intrusion detection systems to predict traffic traces identified with malicious attacks. The results are validated by matching predictions to existing denylists of published malicious IP addresses and deep packet inspection. The usage of our proposed novel distributional features, combined with techniques that enable modelling complex input feature spaces result in highly accurate predictions by our trained models.Comment: Accepted and presented in CAMLIS 2022, https://www.camlis.org/2022-conference. arXiv admin note: text overlap with arXiv:2108.0892

Modulation of functional properties of laforin phosphatase by alternative splicing reveals a novel mechanism for the EPM2A gene in Lafora progressive myoclonus epilepsy

The EPM2A gene, encoding the dual-phosphatase laforin, is mutated in a fatal form of progressive myoclonus epilepsy known as Lafora disease (LD). The EPM2A gene, by differential splicing of its transcripts, is known to encode two laforin isoforms having distinct carboxyl termini; a major isoform localized in the cytoplasm (laf331), and a minor isoform that is targeted to the nucleus as well (laf317). We show here that the two laforin isoforms interact with each other and form homo and heterodimers. The homodimer of laf331 display robust phosphatase activity, whereas the laf317 homodimer and the laf331–laf317 heterodimer lack phosphatase activity. Laf331 binds to glycogen only as a monomeric form. Laf317, on the other hand, was unable to bind to glycogen as a homodimer or as a heterodimer. Similar to laf331, laf317 interacts with and functions as a substrate for the malin ubiquitin ligase—a product of another gene defective in LD. Malin, however, shows higher affinity towards laf331 when compared with laf317. We have also tested the effect of LD-associated mutations, whose effects are restricted to the laf331 isoform, on laf331–laf317 interaction. Two such mutations are known and both abolish the interactions between laf317 and laf331 and their heterodimerization, but not the homodimerization property of laf331. Thus, laf317 could function as a dominant-negative regulator of laf331, and laf331-specific mutations might affect laf317 functions as well. Thus, our findings reveal a novel mechanism for the EPM2A gene function, regulated by alternative splicing, in normal as well as disease conditions

Identification and characterization of novel splice variants of the human EPM2A gene mutated in Lafora progressive myoclonus epilepsy

The EPM2A gene, defective in the fatal neurodegenerative disorder Lafora disease (LD), is known to encode two distinct proteins by differential splicing; a phosphatase active cytoplasmic isoform and a phosphatase inactive nuclear isoform. We report here the identification of three novel EPM2A splice variants with potential to code for five distinct proteins in alternate reading frames. These novel isoforms, when ectopically expressed in cell lines, show distinct subcellular localization, interact with and serve as substrates of malin ubiquitin ligase—the second protein defective in LD. Two phosphatase active isoforms interact to form a heterodimeric complex that is inactive as a phosphatase in vitro, suggesting an antagonistic function for laforin isoforms if expressed endogenously in significant amounts in human tissues. Thus alternative splicing could possibly be one of the mechanisms by which EPM2A may regulate the cellular functions of the proteins it codes for

Activation of serum/glucocorticoid-induced kinase 1 (SGK1) underlies increased glycogen levels, mTOR activation, and autophagy defects in Lafora disease

Lafora disease (LD), a fatal genetic form of myoclonic epilepsy, is characterized by abnormally high levels of cellular glycogen and its accumulation as Lafora bodies in affected tissues. Therefore the two defective proteins in LD—laforin phosphatase and malin ubiquitin ligase—are believed to be involved in glycogen metabolism. We earlier demonstrated that laforin and malin negatively regulate cellular glucose uptake by preventing plasma membrane targeting of glucose transporters. We show here that loss of laforin results in activation of serum/glucocorticoid-induced kinase 1 (SGK1) in cellular and animals models and that inhibition of SGK1 in laforin-deficient cells reduces the level of plasma membrane-bound glucose transporter, glucose uptake, and the consequent glycogen accumulation. We also provide evidence to suggest that mammalian target of rapamycin (mTOR) activates SGK1 kinase in laforin-deficient cells. The mTOR activation appears to be a glucose-dependent event, and overexpression of dominant-negative SGK1 suppresses mTOR activation, suggesting the existence of a feedforward loop between SGK1 and mTOR. Our findings indicate that inhibition of SGK1 activity could be an effective therapeutic approach to suppress glycogen accumulation, inhibit mTOR activity, and rescue autophagy defects in LD

The laforin-malin complex negatively regulates glycogen synthesis by modulating cellular glucose uptake via glucose transporters

Lafora disease (LD), an inherited and fatal neurodegenerative disorder, is characterized by increased cellular glycogen content and the formation of abnormally branched glycogen inclusions, called Lafora bodies, in the affected tissues, including neurons. Therefore, laforin phosphatase and malin ubiquitin E3 ligase, the two proteins that are defective in LD, are thought to regulate glycogen synthesis through an unknown mechanism, the defects in which are likely to underlie some of the symptoms of LD. We show here that laforin's subcellular localization is dependent on the cellular glycogen content and that the stability of laforin is determined by the cellular ATP level, the activity of 5′-AMP-activated protein kinase, and the affinity of malin toward laforin. By using cell and animal models, we further show that the laforin-malin complex regulates cellular glucose uptake by modulating the subcellular localization of glucose transporters; loss of malin or laforin resulted in an increased abundance of glucose transporters in the plasma membrane and therefore excessive glucose uptake. Loss of laforin or malin, however, did not affect glycogen catabolism. Thus, the excessive cellular glucose level appears to be the primary trigger for the abnormally higher levels of cellular glycogen seen in LD

Lafora disease in the Indian population: EPM2A and NHLRC1 gene mutations and their impact on subcellular localization of laforin and malin

Lafora disease (LD) is a fatal form of teenage-onset autosomal recessive progressive myoclonus epilepsy. LD is more common among geographic isolates and in populations with a higher rate of consanguinity. Mutations in two genes, EPM2A encoding laforin phosphatase, and NHLRC1 encoding malin ubiquitin ligase, have been shown to cause the LD. We describe here a systematic analysis of the EPM2A and the NHLRC1 gene sequences in 20 LD families from the Indian population. We identified 12 distinct mutations in 15 LD families. The identified novel mutations include 4 missense mutations (K140N, L310W, N148Y, and E210 K) and a deletion of exon 3 for EPM2A, and 4 missense mutations (S22R, L279P, L279P, and L126P) and a single base-pair insertional mutation (612insT) for NHLRC1. The EPM2A gene is known to encode two laforin isoforms having distinct carboxyl termini; a major isoform localized in the cytoplasm, and a minor isoform that targeted the nucleus. We show here that the effect of the EPM2A gene mutation L310W was limited to the cytoplasmic isoform of laforin, and altered its subcellular localization. We have also analyzed the impact of NHLRC1 mutations on the subcellular localization of malin. Of the 6 distinct mutants tested, three targeted the nucleus, one formed perinuclear aggregates, and two did not show any significant difference in the subcellular localization as compared to the wild-type malin. Our results suggest that the altered subcellular localization of mutant proteins of the EPM2A and NHLRC1 genes could be one of the molecular bases of the LD phenotype

How different connections in flat FLRW geometry impact energy conditions in f(Q)f(Q) theory?

In this study of the modified $f(Q)$ theory of gravity in the spatially flat Friedmann-Lema\^itre-Robertson-Walker (FLRW) spacetime, we explore all the affine connections compatible with the symmetric teleparallel structure; three classes of such connections exist, each involving an unknown time-varying parameter $\gamma(t)$. Assuming ordinary barotropic fluid as the matter source, we first derive the Friedmann-like pressure and energy equations. Next we impose constraints on the parameters of two separate $f(Q)$ models, $f(Q)=Q+\beta Q^2$ and $f(Q)=Q+\beta\sqrt{-Q}$ from the traditional energy conditions. Observational values of some prominent cosmological parameters are used for this purpose, yielding an effective equation of state $\omega^{eff}=-0.82$.Comment: To be published in the journal "Fortschritte der Physik

Association of ADAM33 gene polymorphisms with adult-onset asthma and its severity in an Indian adult population

ADAM33, a member of the ADAM(a disintegrin and metalloprotease) gene family, is an asthma susceptibility gene originally identified by positional cloning. In the present study, we investigated the possible association of five single-nucleotide polymorphisms (SNPs) in the ADAM33 (rs511898, rs528557, rs44707, rs597980 and rs2787094) with adult-onset asthma in an Indian population. The study included 175 patients with mild intermittent (n=44), mild persistent (n=108) or moderate persistent (n=23) subgroups of asthma, and 253 nonasthmatic control individuals. SNPs were genotyped with the help of restriction fragment length polymorphism polymerase chain reaction (RFLP-PCR) method, and data were analysed using chi-square test and logistic regression model. Bonferroni’s correction for multiple comparisons was applied for each hypothesis. Genotypes and allele frequencies of SNPs rs511898 and rs528557 were significantly associated with adult-onset asthma(P=0.010-<0.001). A significant association of the homozygous mutant genotype and mutant alleles of SNPs rs2787094, rs44707 and rs597980 with the asthma was also observed (P=0.020-<0.001). A positive association between asthma and haplotypes AGCCT, GGCCT, AGACT, GCAGT, GGACT, ACCCC and AGACC were also found (P=0.036-<0.001,OR=2.07–8.49). Haplotypes AGCGT, GCAGC, ACAGC, ACAGT, GGAGC and GGCGT appear to protect against asthma (P=0.013-<0.0001, OR=0.34–0.10). Our data suggest that ADAM33 gene polymorphisms serve as genetic risk factors for asthma in Indian adult population