Population genetic structure and demographic history of the freshwater crab Potamon elbursi (Brachyura: Potamidae) from the Alborz Mountains in northern Iran

<p>Hydrographically separated populations of the freshwater crab <em>Potamon elbursi </em>Pretzmann, 1976 were genetically investigated to assess their local diversity and to reconstruct the possible role of Quaternary glaciations in shaping current diversity in the Alborz Mountains, northern Iran. A total of 61 specimens from six rivers were collected from the two different drainage systems of the Alborz Mountains, Namak Lake and the South Caspian watershed. A comparative analysis of a partial sequence of the mitochondrial cytochrome oxidase subunit I gene revealed relatively high overall haplotype diversity and low nucleotide diversity. In four populations, there is no association between the haplotype network and the geographical separation between drainages, whereas the remaining two populations consist of private haplotypes. Gene flow among rivers was estimated using pairwise differences of <em>Φ</em>st; in almost all cases gene flow was significantly restricted, regardless of association to a particular river system. Surprisingly, the only exception was the pairwise comparison of two distant rivers belonging to different drainages; this lack of differentiation may be attributed to incomplete lineage sorting or secondary introduction events. The mismatch distribution analysis, together with the shape of the haplotype network and the nucleotide and haplotype diversity indices, indicates that the studied metapopulation show the signature of recent population bottlenecks followed by demographic or spatial expansion and dating back to Pleistocene climatic fluctuations. </p

Phylogeography of Potamon ibericum (Brachyura: Potamidae) identifies Quaternary glacial refugia within the Caucasus biodiversity hot spot

Refugia are critical for the maintenance of biodiversity during the periods of Quaternary climatic oscillations. The long-term persistence of refugial populations in a large continuous refugium has resulted in a homogenous pattern of genetic structure among populations, while highly structured evolutionary lineages characterize the restriction of refugial populations to smaller subrefugia. These mechanisms have resulted in the identification of hot spots of biodiversity within putative glacial refugia. We studied phylogeography of Potamon ibericum (Brachyura: Potamidae) in the drainages of the western Caucasus biodiversity hot spot (i.e., Colchis and the Caucasus) to infer spatial genetic structure and potential refugia for a freshwater crab in this region. These areas have traditionally considered as a refugium due to the presence of Tertiary relict species. We integrated population genetic data and historical demographic analysis from cytochrome oxidase subunit I sequences and paleoclimatic data from species distribution modeling (SDM). The results revealed the lack of phylogeographic structure and provided evidence for demographic expansion. The SDM presented a rather homogenous and large refugium that extended from northeast Turkey to Colchis during the last glacial period. In contrast to these findings, previous phylogeographic study on P.ibericum of the eastern Caucasus biodiversity hot spot (i.e., Hyrcania) identified multiple independent refugia. By combining these results, we explain the significance of this important western Palearctic hot spot of biological diversity in shaping the geographic distribution of intraspecific genetic diversity in a freshwater taxon

Diagnosis of early alzheimer&#039;s disease based on EEG source localization and a standardized realistic head model

In this paper, distributed electroencephalographic (EEG) sources in the brain have been mapped with the objective of early diagnosis of Alzheimer&#039;s disease (AD). To this end, records from a montage of a high-density EEG from 17 early AD patients and 17 matched healthy control subjects were considered. Subjects were in eyes-closed, resting-state condition. Cortical EEG sources were modeled by the standardized low-resolution brain electromagnetic tomography (sLORETA) method. Relative logarithmic power spectral density values were obtained in the four conventional frequency bands (alpha, beta, delta, and theta) and 12 cortical regions. Results show that in the left brain hemisphere, the theta band of AD subjects shows an increase in the power, whereas the alpha band shows a decreased activity (P-value &lt;;0.05). In the right brain hemisphere of AD subjects, a decreased activity is observed in all frequency bands. It was also noticed that the right temporal region shows a significant difference between the two groups in all frequency bands. Using a support vector machine, control and patient groups are discriminated with an accuracy of 84.4%, sensitivity 75.0%, and specificity of 93.7%

High-throughput image processing software for the study of nuclear architecture and gene expression

Abstract High-throughput imaging (HTI) generates complex imaging datasets from a large number of experimental perturbations. Commercial HTI software programs for image analysis workflows typically do not allow full customization and adoption of new image processing algorithms in the analysis modules. While open-source HTI analysis platforms provide individual modules in the workflow, like nuclei segmentation, spot detection, or cell tracking, they are often limited in integrating novel analysis modules or algorithms. Here, we introduce the High-Throughput Image Processing Software (HiTIPS) to expand the range and customization of existing HTI analysis capabilities. HiTIPS incorporates advanced image processing and machine learning algorithms for automated cell and nuclei segmentation, spot signal detection, nucleus tracking, nucleus registration, spot tracking, and quantification of spot signal intensity. Furthermore, HiTIPS features a graphical user interface that is open to integration of new analysis modules for existing analysis pipelines and to adding new analysis modules. To demonstrate the utility of HiTIPS, we present three examples of image analysis workflows for high-throughput DNA FISH, immunofluorescence (IF), and live-cell imaging of transcription in single cells. Altogether, we demonstrate that HiTIPS is a user-friendly, flexible, and open-source HTI software platform for a variety of cell biology applications

Quantification of Collagen Organization after Nerve Repair

Background:. Clinical outcomes after nerve injury and repair remain suboptimal. Patients may be plagued by poor functional recovery and painful neuroma at the repair site, characterized by disorganized collagen and sprouting axons. Collagen deposition during wound healing can be intrinsically imaged using second harmonic generation (SHG) microscopy. The purpose of this study was to develop a protocol for SHG imaging of nerves and to assess whether collagen alignment can be quantified after nerve repair. Methods:. Sciatic nerve transection and epineural repair was performed in male rats. The contralateral nerves were used as intra-animal controls. Ten-millimeter nerve segments were harvested and fixed onto slides. SHG images were collected using a 20× objective on a multiphoton microscope. Collagen fiber alignment was calculated using CurveAlign software. Alignment was calculated on a scale from 0 to 1, where 1 represents perfect alignment. Statistical analysis was performed using a linear mixed-effects model. Results:. Eight male rats underwent right sciatic nerve repair using 9-0 Nylon suture. There were gross variations in collagen fiber organization in the repaired nerves compared with the controls. Quantitatively, collagen fibers were more aligned in the control nerves (mean alignment 0.754, SE 0.055) than in the repairs (mean alignment 0.413, SE 0.047; P < 0.001). Conclusions:. SHG microscopy can be used to quantitate collagen after nerve repair via fiber alignment. Given that the development of neuroma likely reflects aberrant wound healing, ex vivo and/or in vivo SHG imaging may be useful for further investigation of the variables predisposing to neuroma