Overexpression of <Emphasis Type="Italic">SNF4</Emphasis> and deletions of <Emphasis Type="Italic">REG1</Emphasis>- and <Emphasis Type="Italic">REG2</Emphasis>-enhanced maltose metabolism and leavening ability of baker’s yeast in lean dough

Maltose metabolism of baker’s yeast (Saccharomyces cerevisiae) in lean dough is suppressed by the glucose effect, which negatively affects dough fermentation. In this study, differences and interactions among SNF4 (encoding for the regulatory subunit of Snf1 kinase) overexpression and REG1 and REG2 (which encodes for the regulatory subunits of the type I protein phosphatase) deletions in maltose metabolism of baker’s yeast were investigated using various mutants. Results revealed that SNF4 overexpression and REG1 and REG2 deletions effectively alleviated glucose repression at different levels, thereby enhancing maltose metabolism and leavening ability to varying degrees. SNF4 overexpression combined with REG1/REG2 deletions further enhanced the increases in glucose derepression and maltose metabolism. The overexpressed SNF4 with deleted REG1 and REG2 mutant ΔREG1ΔREG2?+?SNF4 displayed the highest maltose metabolism and strongest leavening ability under the test conditions. Such baker’s yeast strains had excellent potential applications.     

<Emphasis Type="Italic">ABI3</Emphasis> and <Emphasis Type="Italic">PLCG2</Emphasis> missense variants as risk factors for neurodegenerative diseases in Caucasians and African Americans

Background

Rare coding variants ABI3_rs616338-T and PLCG2_rs72824905-G were identified as risk or protective factors, respectively, for Alzheimer’s disease (AD).

Methods

We tested the association of these variants with five neurodegenerative diseases in Caucasian case-control cohorts: 2742 AD, 231 progressive supranuclear palsy (PSP), 838 Parkinson’s disease (PD), 306 dementia with Lewy bodies (DLB) and 150 multiple system atrophy (MSA) vs. 3351 controls; and in an African-American AD case-control cohort (181 AD, 331 controls). 1479 AD and 1491 controls were non-overlapping with a prior report.

Results

Using Fisher’s exact test, there was significant association of both ABI3_rs616338-T (OR?=?1.41, p?=?0.044) and PLCG2_rs72824905-G (OR?=?0.56, p?=?0.008) with AD. These OR estimates were maintained in the non-overlapping replication AD-control analysis, albeit at reduced significance (ABI3_rs616338-T OR?=?1.44, p?=?0.12; PLCG2_rs72824905-G OR?=?0.66, p?=?0.19). None of the other cohorts showed significant associations that were concordant with those for AD, although the DLB cohort had suggestive findings (Fisher’s test: ABI3_rs616338-T OR?=?1.79, p?=?0.097; PLCG2_rs72824905-G OR?=?0.32, p?=?0.124). PLCG2_rs72824905-G showed suggestive association with pathologically-confirmed MSA (OR?=?2.39, p?=?0.050) and PSP (OR?=?1.97, p?=?0.061), although in the opposite direction of that for AD. We assessed RNA sequencing data from 238 temporal cortex (TCX) and 224 cerebellum (CER) samples from AD, PSP and control patients and identified co-expression networks, enriched in microglial genes and immune response GO terms, and which harbor PLCG2 and/or ABI3. These networks had higher expression in AD, but not in PSP TCX, compared to controls. This expression association did not survive adjustment for brain cell type population changes.

Conclusions

We validated the associations previously reported with ABI3_rs616338-T and PLCG2_rs72824905-G in a Caucasian AD case-control cohort, and observed a similar direction of effect in DLB. Conversely, PLCG2_rs72824905-G showed suggestive associations with PSP and MSA in the opposite direction. We identified microglial gene-enriched co-expression networks with significantly higher levels in AD TCX, but not in PSP, a primary tauopathy. This co-expression network association appears to be driven by microglial cell population changes in a brain region affected by AD pathology. Although these findings require replication in larger cohorts, they suggest distinct effects of the microglial genes, ABI3 and PLCG2 in neurodegenerative diseases that harbor significant vs. low/no amyloid ß pathology.

     

Genetic Association of <Emphasis Type="Italic">HLA</Emphasis> Gene Variants with MRI Brain Structure in Alzheimer’s Disease

There is accumulating evidence that the human leukocyte antigen (HLA) gene variants are associated with Alzheimer’s disease (AD). However, how they affect AD occurrence is still unknown. In this study, we firstly investigated the association of gene variants in HLA gene variants and brain structures on MRI in a large sample from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) to explore the effects of HLA on AD pathogenesis. We selected hippocampus, hippocampus CA1 subregion, parahippocampus, posterior cingulate, precuneus, middle temporal, entorhinal cortex, and amygdala as regions of interest (ROIs). According to the previous association studies of HLA variants and AD, 12 SNPs in HLA were identified in the dataset following quality control measures. In total group analysis, our results showed that TNF-α SNPs at rs2534672 and rs2395488 were significantly positively associated with the volume of the left middle temporal lobe (rs2534672: P?=?0.00035, Pc?=?0.004; rs2395488: P?=?0.0038, Pc?=?0.023) at baseline. In the longitudinal study, HFE rs1800562 was remarkably correlated with the lower atrophy rate of right middle temporal lobe (P?=?0.0003, Pc?=?0.003) and RAGE rs2070600 was associated with the atrophy rate of right hippocampus substructure-CA1 over 2 years (P?=?0.003, Pc?=?0.035). Furthermore, we detected the above four associations in mild cognitive impairment (MCI) subgroup analysis, as well as the association of rs2534672 with the baseline volume of the left middle temporal lobe in normal cognition (NC) subgroup analysis. Our study provided preliminary evidences that HLA gene variants might participate in the structural alteration of AD associated brain regions, hence modulating the susceptibility of AD.     

Occupancy modeling of <Emphasis Type="Italic">Parnassius clodius</Emphasis> butterfly populations in Grand Teton National Park,Wyoming

Estimating occupancy patterns and identifying vegetation characteristics that influence the presence of butterfly species are essential approaches needed for determining how habitat changes may affect butterfly populations in the future. The montane butterfly species, Parnassius clodius, was investigated to identify patterns of occupancy relating to habitat variables in Grand Teton National Park and Bridger-Teton National Forest, Wyoming, United States. A series of presence–absence surveys were conducted in 2013 in 41 mesic to xeric montane meadows that were considered suitable habitat for P. clodius during their flight season (June–July) to estimate occupancy (ψ) and detection probability (p). According to the null constant parameter model, P. clodius had high occupancy of ψ?=?0.78?±?0.07 SE and detection probability of p?=?0.75?±?0.04 SE. In models testing covariates, the most important habitat indicator for the occupancy of P. clodius was a strong negative association with big sagebrush (Artemisia tridentata; β = ??21.39?±?21.10 SE) and lupine (Lupinus spp.; β?=???20.03?±?21.24 SE). While P. clodius was found at a high proportion of meadows surveyed, the presence of A. tridentata may limit their distribution within montane meadows at a landscape scale because A. tridentata dominates a large percentage of the montane meadows in our study area. Future climate scenarios predicted for high elevations globally could cause habitat shifts and put populations of P. clodius and similar non-migratory butterfly populations at risk.     

Distribution of manganese and other biometals in <Emphasis Type="Italic">flatiron</Emphasis> mice

Flatiron (ffe) mice display features of “ferroportin disease” or Type IV hereditary hemochromatosis. While it is known that both Fe and Mn metabolism are impaired in flatiron mice, the effects of ferroportin (Fpn) deficiency on physiological distribution of these and other biometals is unknown. We hypothesized that Fe, Mn, Zn and/or Cu distribution would be altered in ffe/+ compared to wild-type (+/+) mice. ICP-MS analysis showed that Mn, Zn and Cu levels were significantly reduced in femurs from ffe/+ mice. Bone deposits reflect metal accumulation, therefore these data indicate that Mn, Zn and Cu metabolism are affected by Fpn deficiency. The observations that muscle Cu, lung Mn, and kidney Cu and Zn levels were reduced in ffe/+ mice support the idea that metal metabolism is impaired. While all four biometals appeared to accumulate in brains of flatiron mice, significant gender effects were observed for Mn and Zn levels in male ffe/+ mice. Metals were higher in olfactory bulbs of ffe/+ mice regardless of gender. To further study brain metal distribution, ⁵⁴MnCl₂ was administered by intravenous injection and total brain ⁵⁴Mn was measured over time. At 72 h, ⁵⁴Mn was significantly greater in brains of ffe/+ mice compared to +/+ mice while blood ⁵⁴Mn was cleared to the same levels by 24 h. Taken together, these results indicate that Fpn deficiency decreases Mn trafficking out of the brain, alters body Fe, Mn, Zn and Cu levels, and promotes metal accumulation in olfactory bulbs.     

Planarian homolog of puromycin-sensitive aminopeptidase <Emphasis Type="Italic">DjPsa</Emphasis> is required for brain regeneration

Puromycin-sensitive aminopeptidase (PSA) belongs to the M1 zinc metallopeptidase family. PSA is the most abundant aminopeptidase in the brain and plays a role in the metabolism of neuropeptides including those involved in neurodegeneration. A cDNA DjPsa was identified from the planarian Dugesia japonica cDNA library. It contains a 639-bp open reading frame corresponding to a deduced protein of 212 amino acids. Whole mount in situ hybridization revealed that DjPsa is expressed in the brain and ventral nerve cords of intact and regenerating animals and demonstrates a tissue and stage-specific expression pattern of DjPsa in developing embryos and larvae. Knocking down DjPsa gene expression with RNA interference during planarian regeneration inhibits the brain reformation completely. The results suggest that DjPsa is required for planarian brain regeneration.     

Chaotic Dynamics of Neuromuscular System Parameters and the Problems of the Evolution of Complexity

The evolution rate v(t) varies among diverse biosystems, but a general theory can be formulated when the dynamics of the biosystem stater x = x(t) = (x₁, x₂, x _m ) ^T is considered in the m-dimensional space of states. A mathematical approach is proposed for evaluating such processes and describes the processes in terms of particular chaos of the statistical distribution functions f(x). In the case of complex multicomponent systems with a high dimension number m (m ?1) of the phase space of states, we propose using pairwise comparison matrices of samples x(t) when homeostasis is constant and calculating the parameters of quasiattractors. The Glensdorff–Prigogine thermodynamic approach to estimating evolution is inefficient in assessing the third-type systems, while it is applicable and the Prigogine theorem works at the level of molecular systems. Alterations in the state of the human neuromuscular system were found to lead to chaotic changes in the statistical functions f(x) in tremor recording samples, while quasiattractor parameters demonstrate a certain regularity.     

Definition of unit internal (physiological) time

We provide a definition of the unit internal (physiological) time based on metabolism. If q(t) is specific rate of metabolism, i.e. the amount of energy (oxygen) consumed by unit of active mass per physical time unit, the unit of physiological time τ(t) is defined as physical time, during which unit of active mass consumes one unit of energy: τ(t) = 1/q(t). The dimension of unit physiological time is the same as that of unit physical time and its value depends on q(t). Therefore, the unit physiological time τ(t) is a variable value, while the internal time is unequal relative to the physical time. The more internal time units τ, i.e., elementary acts of energy consumption, fit in the unit physical time t, the longer is the unit physical time for the unit active mass relative to the internal time unit, i.e., the physical time is seemingly slowed down. And, on the contrary, the less elementary acts of energy consumption take place during unit physical time, the shorter seems unit t, i.e. physical time is seemingly accelerated. Unequal course of the internal time is determined by the curve of specific metabolism q(t) during the life under specific conditions and, hence, internal time is individual. It has been questioned that the total (during lifetime) specific metabolism, often called Rubner constant, can serve as specie specific characteristic.     

Molecular characterization and expression of suppressor of cytokine signaling (SOCS) 1, 2 and 3 under acute hypoxia and reoxygenation in pufferfish, <Emphasis Type="Italic">Takifugu fasciatus</Emphasis>

Hypoxia seriously affects the innate immune system of fish. However, the roles of suppressor of cytokine signaling (SOCS), pivotal anti-inflammatory genes, in response to hypoxia/reoxygenation remain largely unexplored. The primary objective of this study was to elucidate the function of SOCS genes under acute hypoxia and reoxygenation in pufferfish (Takifugu fasciatus). In the present study, SOCS1, 2 and 3 were identified in T. fasciatus referred to as TfSOCS1, 2 and 3. Then, qRT-PCR and western blot analysis were employed to assess their expressions at both the mRNA and protein levels. Tissue distribution demonstrated that the three SOCS genes were predominantly distributed in gill, brain and liver. Under hypoxia challenge (1.63?±?0.2 mg/L DO for 2, 4, 6 and 8 h), the expressions of TfSOCS1 and 3 in brain and liver at the mRNA and protein levels were significantly decreased, while their expressions showed an opposite trend in gill. Different from the expressions of TfSOCS1 and 3, the expression of TfSOCS2 was inhibited in gill, along with its increased expression in brain and liver. After normoxic recovery (7.0?±?0.3 mg/L of DO for 4 and 12 h), most of TfSOCS genes were significantly altered at R4 (reoxygenation for 4 h) and returned to the normal level at R12 (reoxygenation for 12 h). SOCS genes played vital roles in response to hypoxia/reoxygenation challenge. Our findings greatly strengthened the relation between innate immune and hypoxia stress in T. fasciatus.     

Synergic effects of the <Emphasis Type="Italic">ApoC3</Emphasis> and <Emphasis Type="Italic">ApoA4</Emphasis> polymorphisms on the risk of hypertension

The apolipoprotein (Apo) C3 and A4 genes, which are members of the ApoA1/C3/A4/A5 gene cluster, play important roles in lipid metabolism. Despite their importance, studies on the association between these polymorphisms in patients with hypertension are rare. In this study, we examined the associations of ApoC3 (?482C>T rs2854117, ?455T>C rs2854116 and 3238G>C rs5128) and ApoA4 1687A>G rs5104 polymorphisms in Korean hypertensive patients. Three hundred and forty patients with hypertension and 515 healthy normotensive subjects were studied. ApoC3 and ApoA4 polymorphisms in the subjects were analyzed by polymerase chain reaction and restriction fragment length polymorphism. The four polymorphisms were not associated with susceptibility to hypertension. However, several haplotypes constructed from four polymorphisms of the ApoC3 and ApoA4 genes were associated with susceptibility to hypertension. With respect to the clinical parameters of hypertension, the ?482C>T and ?455T>C polymorphisms of the ApoC3 gene were associated with abnormal body mass index (P?=?0.024) and triglyceride levels (P?=?0.033) in the hypertensive group, respectively. Based on these results, the ApoC3 and ApoA4 polymorphisms might affect synergically susceptibility to hypertension in Koreans.     

Detection of Insertions/Deletions Within <Emphasis Type="Italic">SIRT1</Emphasis>, <Emphasis Type="Italic">SIRT2</Emphasis> and <Emphasis Type="Italic">SIRT3</Emphasis> Genes and Their Associations with Body Measurement Traits in Cattle

Growth traits are complex quantitative traits controlled by numerous candidate genes, and they can be well-evaluated using body measurement traits. As the members of the nicotinamide adenine dinucleotide-dependent family of histone deacetylases, class I sirtuin genes (including SIRT1, SIRT2 and SIRT3) play crucial roles in regulating lipid metabolism, cellular growth and metabolism, suggesting that they are potential candidate genes affecting body measurement traits in animals. Hence, the objective of this work aimed to detect novel insertions/deletions (indels) of SIRT1, SIRT2 and SIRT3 genes in 955 cattle belonging to five breeds, as well as to evaluate their effects on body measurement traits. Herein, the novel 12-bp indel of SIRT1 gene, the 7-bp indel of SIRT2 gene and the 26-bp indel of SIRT3 gene were firstly reported, respectively. The association analysis indicated that the indels within SIRT1 and SIRT2 genes were significantly associated with body measurement traits such as body weight, chest circumference, height at hip cross, hip width, body height, etc. (P?<?0.05 or P?<?0.01). Therefore, based on these findings, the two novel indel variants within bovine SIRT1 and SIRT2 genes could be considered as potential molecular markers for growth traits in cattle selection practices and breeding.     

Function and regulation of tau conformations in the development and treatment of traumatic brain injury and neurodegeneration

One of the two common hallmark lesions of Alzheimer’s disease (AD) brains is neurofibrillary tangles (NFTs), which are composed of hyperphosphorylated tau protein (p-tau). NFTs are also a defining feature of other neurodegenerative disorders and have recently been identified in the brains of patients suffering from chronic traumatic encephalopathy (CTE). However, NFTs are not normally observed in traumatic brain injury (TBI) until months or years after injury. This raises the question of whether NFTs are a cause or a consequence of long-term neurodegeneration following TBI. Two conformations of phosphorylated tau, cis p-tau and trans p-tau, which are regulated by the peptidyl-prolyl isomerase Pin1, have been previously identified. By generating a polyclonal and monoclonal antibody (Ab) pair capable of distinguishing between cis and trans isoforms of p-tau (cis p-tau and trans p-tau, respectively), cis p-tau was identified as a precursor of tau pathology and an early driver of neurodegeneration in AD, TBI and CTE. Histological studies shows the appearance of robust cis p-tau in the early stages of human mild cognitive impairment (MCI), AD and CTE brains, as well as after sport- and military-related TBI. Notably, cis p-tau appears within hours after closed head injury and long before other known pathogenic p-tau conformations including oligomers, pre-fibrillary tangles and NFTs. Importantly, cis p-tau monoclonal antibody treatment not only eliminates cis p-tau induction and tau pathology, but also restores many neuropathological and functional outcome in TBI mouse models. Thus, cis p-tau is an early driver of tau pathology in TBI and CTE and detection of cis p-tau in human bodily fluids could potentially provide new diagnostic and prognostic tools. Furthermore, humanization of the cis p-tau antibody could ultimately be developed as a new treatment for AD, TBI and CTE.     

Expression of iron-regulators in the bone tissue of rats with and without iron overload

Recently, more and more studies indicate that iron overload would cause osteopenia or osteoporosis. However, the molecular mechanism of it remains unclear. Moreover, very little is known about the iron metabolism in bone tissue at present. Therefore, the mRNA expression of iron-regulators, transferrin receptor1 (Tfr1), divalent metal transporter1 (Dmt1?+?IRE and Dmt1???IRE), ferritin (FtH and FtL), and ferroportin1 (Ireg1), and the localization of ferroportin1 protein were examined in the bone tissue of rats. In addition, the mRNA expression of each gene was compared between groups of rats with and without iron overload. The results showed that ferroportin1 protein was localized in the cytoplasm of osteoblast, osteocyte, chondrocyte and osteoclast of rats’ femur. The six iron-regulatory genes, Tfr1, ferritin (FtH and FtL), (Dmt1?+?IRE and Dmt1???IRE) and ferroportin1 (Ireg1), were found in femurs of rats. In addition, significantly up-regulated expression of FtH and FtL mRNA, and markedly down-regulated expression of Tfr1, Dmt1?+?IRE and Ireg1 mRNA, were observed in the iron overload group compared with the control group. The result indicates that ferroportin1 protein is localized in the cytoplasm of bone cells of rats. Tfr1, Dmt1, ferritin and ferroportin1 exist in bone tissue of rats, and they may be involved in the pathological process of iron overload-induced bone lesion.     

Bioinformatic prediction and analysis of glucolipid metabolic regulation by miR-34a in <Emphasis Type="Italic">Megalobrama amblycephala</Emphasis>

The objective of this study was to analyze the target genes and regulatory function of miR-34a in Megalobrama amblycephala using second-generation high-throughput sequencing and bioinformatic tools. Functional enrichment analysis was performed by gene ontology. MiR-34a and target gene expression levels were measured in M. amblycephala fed normal and high-carbohydrate diets. The results revealed that miR-34a was highly conserved in several species, and miR-34a of M. amblycephala has a close evolutionary relationship to that of zebrafish and common carp. miRanda, TargetScan, RNAhybrid predicted 5,185, 6,282 and 2,168 target genes, respectively, and 645 target genes were in common. According to annotation information, the target genes were enriched in phosphate metabolism, glycerophospholipid metabolism, Golgi vesicle transport, cell division, and other biological processes (P?<?0.05). Pathway enrichment analysis revealed that these target genes were mainly enriched in alpha-linolenic acid and linoleic acid metabolism, ether lipid metabolism, VEGF signaling pathway, Fc epsilon RI signaling pathway, GnRH signaling pathway, and MAPK signaling pathway (P?<?0.05). The regulatory role of miR-34a was more significant in the liver than in the brain of M. amblycephala. MiR-34a regulates glucose lipid homeostasis induced by high glucose diets by upregulating hepatic PI3K/Akt, FOXO, and TOR signaling pathways.